From aea53c6ea5edde1ce1ff12e9534cf135f100740c Mon Sep 17 00:00:00 2001 From: emullier Date: Thu, 8 Aug 2024 09:45:03 +0200 Subject: [PATCH 01/26] [fix] Update test_output1 circleci --- .../ds-sample_test-01_outputs.txt | 2865 ++++++++++++++++- 1 file changed, 2722 insertions(+), 143 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt index 35c5965a..1beecb2e 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt @@ -1,50 +1,1896 @@ +cmp-v3.1.0/dataset_description.json +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz +cmp-v3.1.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval +cmp-v3.1.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec +cmp-v3.1.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json +cmp-v3.1.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz +cmp-v3.1.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json +cmp-v3.1.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json +cmp-v3.1.0/sub-01/ses-01/sub-01_ses-01_log.txt cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt +cmp-v3.2.0-mapmri/cmp-v3.2.0/dataset_description.json +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_fMRI_config.json +cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt +cmp-v3.2.0-mapmri/freesurfer-7.1.1/dataset_description.json +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA3a_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA3a_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA3b_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA3b_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA44_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA44_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA45_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA45_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA4a_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA4a_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA4p_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA4p_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA2_exvivo.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA2_exvivo.thresh.label +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA3a_exvivo.label 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+cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/cc_up.lta +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.auto.xfm +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.auto.xfm.lta +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_avi.log +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_avi_QA.log +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log.old +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/ponscc.cut.log +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.cmd +cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.done 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+freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.label @@ -65,25 +1911,35 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot 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+freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -232,6 +2105,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels +freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -239,18 +2113,19 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial +freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.premesh 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+nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/_node.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/_report/report.rst +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/result_T1_skullstrip.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/sub-01_ses-01_desc-head_T1w_brain.nii.gz From 0f4e38788d2cf0099420502b385f7975f1e74836 Mon Sep 17 00:00:00 2001 From: emullier Date: Thu, 8 Aug 2024 11:45:13 +0200 Subject: [PATCH 02/26] [fix] Update test_output1 and test4_output circleci --- .../ds-sample_test-01_outputs.txt | 2538 +---------------- .../ds-sample_test-04_outputs.txt | 696 ++--- 2 files changed, 350 insertions(+), 2884 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt index 1beecb2e..c538ca64 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt @@ -1,1787 +1,4 @@ -cmp-v3.1.0/dataset_description.json -cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml -cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv -cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt -cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml -cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv -cmp-v3.1.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt 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-cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_fMRI_config.json -cmp-v3.2.0-mapmri/cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt -cmp-v3.2.0-mapmri/freesurfer-7.1.1/dataset_description.json -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label 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-cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.label 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-cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA4a_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA4p_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA4p_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aseg.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aseg.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aseg.presurf.hypos.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/aseg.presurf.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/brain.finalsurfs.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/brainmask.auto.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/brainmask_eroded.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/brainmask.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/brainmask.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/brain.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/brain.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/lh.ribbon.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log.bak -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/norm.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/nu.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/orig/001.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/orig.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/orig_nu.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/rh.ribbon.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.ni.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.ni.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/segment.dat -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/surface.defects.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/talairach.label_intensities.txt -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/talairach.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/talairach_with_skull.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/cc_up.lta -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.auto.xfm -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.auto.xfm.lta -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_avi.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_avi_QA.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log.old -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/ponscc.cut.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.cmd -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.done -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.local-copy -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/recon-config.yaml -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/scripts/unknown-args.txt -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/aseg.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/brainvol.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.a2009s.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.DKTatlas.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.pial.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/lh.BA_exvivo.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/lh.BA_exvivo.thresh.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/lh.curv.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/lh.w-g.pct.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/rh.aparc.a2009s.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/rh.aparc.DKTatlas.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/rh.aparc.pial.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/rh.aparc.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.area -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.avg_curv -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels -cmp-v3.2.0-mapmri/freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset 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+cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-CSF_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_label-WM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval @@ -65,22 +67,27 @@ cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz 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freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab +freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.label @@ -101,25 +108,35 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label 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+freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA2_exvivo.label @@ -140,45 +157,36 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label 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freesurfer-7.1.1/sub-01_ses-01/surf/rh.sulc @@ -335,16 +373,14 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.white freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.K +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.Lausanne2018.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.mgz +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.native.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale1_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.Lausanne2018.native.nii.gz -freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.native.nii.gz 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2f7ee4657b36937cc251bf9e27115fee5003c175 Mon Sep 17 00:00:00 2001 From: emullier Date: Thu, 8 Aug 2024 13:43:54 +0200 Subject: [PATCH 03/26] [fix] Update test_output1 awithout dwi and func files --- .../ds-sample_test-01_outputs.txt | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt index c538ca64..2d71d41d 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt @@ -37,24 +37,6 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale2_dseg.nii.gz 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| 36 +++++ .../ref_diffusion_config2.json | 145 +++++++++++++++++ .../ref_diffusion_config_1.json | 146 ++++++++++++++++++ .../ref_diffusion_config_3.json | 142 +++++++++++++++++ .../ref_diffusion_config_4.json | 142 +++++++++++++++++ .../ref_diffusion_config_5.json | 137 ++++++++++++++++ .../ref_fMRI_config_1.nii.json | 81 ++++++++++ .../ref_fMRI_config_2.json | 81 ++++++++++ 8 files changed, 910 insertions(+) create mode 100644 .circleci/tests/configuration_files/ref_anatomical_config_2.json create mode 100644 .circleci/tests/configuration_files/ref_diffusion_config2.json create mode 100644 .circleci/tests/configuration_files/ref_diffusion_config_1.json create mode 100644 .circleci/tests/configuration_files/ref_diffusion_config_3.json create mode 100644 .circleci/tests/configuration_files/ref_diffusion_config_4.json create mode 100644 .circleci/tests/configuration_files/ref_diffusion_config_5.json create mode 100644 .circleci/tests/configuration_files/ref_fMRI_config_1.nii.json create mode 100644 .circleci/tests/configuration_files/ref_fMRI_config_2.json diff --git a/.circleci/tests/configuration_files/ref_anatomical_config_2.json b/.circleci/tests/configuration_files/ref_anatomical_config_2.json new file mode 100644 index 00000000..b6fbb8ee --- /dev/null +++ b/.circleci/tests/configuration_files/ref_anatomical_config_2.json @@ -0,0 +1,36 @@ +{ + "Global": { + "subject_session" : "ses-01", + "subjects" : ["sub-01"], + "process_type" : "anatomical", + "subject" : "sub-01" + }, + "segmentation_stage": { + "make_isotropic": false, + "isotropic_interpolation": "cubic", + "isotropic_vox_size" : 1.0, + "brain_mask_extraction_tool" : "Freesurfer", + "seg_tool" : "Freesurfer", + "use_fsl_brain_mask" : false, + "use_existing_freesurfer_data" : false, + "number_of_threads" : 2 + }, + + "parcellation_stage": { + "parcellation_scheme" : "NativeFreesurfer", + "segment_hippocampal_subfields" : true, + "segment_brainstem" : true, + "ants_precision_type" : "float", + "include_thalamic_nuclei_parcellation" : true, + "pipeline_mode" : "Diffusion", + "parcellation_scheme_editor" : ["NativeFreesurfer", "Lausanne2018", "Custom"], + "number_of_regions" : 0, + "pre_custom" : "Lausanne2018" + }, + + "Multi-processing": { + "number_of_cores" : 1 + } + +} + diff --git a/.circleci/tests/configuration_files/ref_diffusion_config2.json b/.circleci/tests/configuration_files/ref_diffusion_config2.json new file mode 100644 index 00000000..be17868f --- /dev/null +++ b/.circleci/tests/configuration_files/ref_diffusion_config2.json @@ -0,0 +1,145 @@ +{ + "Global": { + "process_type": "diffusion", + "subject_session": "ses-01", + "diffusion_imaging_model": "DSI", + "dmri_bids_acq": "DSI", + "subjects": ["sub-01"], + "subject": "sub-01" + }, + + "diffusion_stage": { + "tracking_processing_tool_editor": ["Dipy", "MRtrix", "Custom"], + "tracking_processing_tool": "MRtrix", + "dilation_kernel": "Box", + "recon_processing_tool_editor": ["Dipy", "Custom"], + 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+"preprocessing_stage": { + "eddy_current_and_motion_correction": true, + "description": "description", + "denoising": true, + "total_readout": 0.0, + "eddy_correct_motion_correction": true, + "dipy_noise_model": "Rician", + "denoising_algo": "MRtrix [MP-PCA]", + "bias_field_algo": "ANTS N4", + "bias_field_correction": true, + "fast_use_priors": true, + "resampling": [3, 3, 3], + "partial_volume_estimation": true, + "eddy_correction_algo": "FSL eddy_correct", + "interpolation": "interpolate" + }, + +"connectome_stage": { + "circular_layout": false, + "output_types": ["gpickle", "mat", "graphml"], + "compute_curvature": false, + "log_visualization": true, + "connectivity_metrics": ["Fiber number", "Fiber length", "Fiber density", "Fiber proportion", "Normalized fiber density" , "ADC", "gFA"] + }, + + +"registration_stage": { + "ants_convergence_winsize" : 10, + "ants_nonlinear_update_field_variance" : 3.0, + "contrast_type" : "dti", + "ants_upper_quantile" : 0.995, + "use_float_precision" : false, + "ants_nonlinear_total_field_variance" : 0.0, + "registration_mode" : "ANTs", + "init" : "header", + "ants_interpolation" : "BSpline", + "ants_linear_sampling_perc" : 0.25, + "apply_to_eroded_wm" : true, + "ants_convergence_thresh" : 1e-06, + "ants_multilab_interpolation_parameters" : [5, 5], + "ants_gauss_interpolation_parameters" : [5, 5], + "ants_nonlinear_cost" : "CC", + "ants_bspline_interpolation_parameters" : [3], + "apply_to_eroded_brain" : false, + "uses_qform" : true, + "pipeline" : "Diffusion", + "ants_lower_quantile" : 0.005, + "no_search" : true, + "ants_linear_cost" : "MI", + "ants_linear_gradient_step" : 0.1, + "apply_to_eroded_csf" : true, + "ants_perform_syn" : true, + "ants_linear_sampling_strategy" : "Regular", + "dof" : 6, + "fsl_cost" : "normmi", + "ants_nonlinear_gradient_step" : 0.1 + + }, + + "Multi-processing": { + "number_of_cores" : 1 + } +} + + diff --git a/.circleci/tests/configuration_files/ref_diffusion_config_1.json b/.circleci/tests/configuration_files/ref_diffusion_config_1.json new file mode 100644 index 00000000..429e4eab --- /dev/null +++ b/.circleci/tests/configuration_files/ref_diffusion_config_1.json @@ -0,0 +1,146 @@ + +{ + "Global": { + "process_type": "diffusion", + "subject_session": "ses-01", + "diffusion_imaging_model": "DSI", + "dmri_bids_acq": "DSI", + "subjects": ["sub-01"], + "subject": "sub-01" + }, + + "diffusion_stage": { + "tracking_processing_tool_editor": ["Dipy", "MRtrix", "Custom"], + "tracking_processing_tool": "MRtrix", + "dilation_kernel": "Box", + "recon_processing_tool_editor": ["Dipy", "Custom"], + "dilation_radius": 1, + "diffusion_model": "Deterministic", + "dilate_rois": true, + "recon_processing_tool": "Dipy", + "dipy_tracking_config.fa_thresh": 0.2, + "dipy_tracking_config.seed_density": 1.0, + "dipy_tracking_config.number_of_seeds": 1000, + "dipy_tracking_config.tracking_mode": "Deterministic", + "dipy_tracking_config.use_act": false, + "dipy_tracking_config.imaging_model": "DSI", + "dipy_tracking_config.sh_order": 8, + "dipy_tracking_config.curvature": 0.0, + "dipy_tracking_config.step_size": 0.5, + "dipy_tracking_config.seed_from_gmwmi": false, + "dipy_tracking_config.sd": true, + "dipy_tracking_config.max_angle": 25.0, + "diffusion_imaging_model_editor": ["DSI", "DTI", "HARDI"], + "mrtrix_tracking_config.min_length": 5, + "mrtrix_tracking_config.angle": 45, + "mrtrix_tracking_config.tracking_mode": "Deterministic", + "mrtrix_tracking_config.use_act": true, + "mrtrix_tracking_config.cutoff_value": 0.05, + "mrtrix_tracking_config.backtrack": false, + "mrtrix_tracking_config.curvature": 0.0, + "mrtrix_tracking_config.crop_at_gmwmi": true, + "mrtrix_tracking_config.step_size": 0.5, + "mrtrix_tracking_config.max_length": 500, + "mrtrix_tracking_config.desired_number_of_tracks": 200000, + "mrtrix_tracking_config.seed_from_gmwmi": false, + "mrtrix_tracking_config.sd": true, + "mrtrix_tracking_config.sift": true, + "mrtrix_recon_config.recon_mode": "Probabilistic", + "mrtrix_recon_config.imaging_model": "DSI", + "mrtrix_recon_config.single_fib_thr": 0.7, + "mrtrix_recon_config.lmax_order": "Auto", + "mrtrix_recon_config.local_model_editor": {"true": "Constrained Spherical Deconvolution"}, + "mrtrix_recon_config.local_model": true, + "mrtrix_recon_config.normalize_to_b0": false, + "diffusion_model_editor": ["Deterministic", "Probabilistic"], + "dipy_recon_config.shore_radial_order": 4, + "dipy_recon_config.shore_constrain_e0": false, + "dipy_recon_config.positivity_constraint": true, + "dipy_recon_config.tracking_processing_tool": "MRtrix", + "dipy_recon_config.imaging_model": "DSI", + "dipy_recon_config.small_delta": 0.02, + "dipy_recon_config.big_delta": 0.5, + "dipy_recon_config.lmax_order": "Auto", + "dipy_recon_config.shore_lambdal": 1e-08, + "dipy_recon_config.shore_lambdan": 1e-08, + "dipy_recon_config.local_model_editor": {"false": "1:Tensor", "true": "2:Constrained Spherical Deconvolution "}, + "dipy_recon_config.shore_zeta": 700, + "dipy_recon_config.local_model": true, + "dipy_recon_config.radial_order": 8, + "dipy_recon_config.radial_order_values": [2, 4, 6, 8, 10, 12], + "dipy_recon_config.single_fib_thr": 0.7, + "dipy_recon_config.recon_mode": "Probabilistic", + "dipy_recon_config.shore_tau": 0.0441759, + "dipy_recon_config.laplacian_regularization": true, + "dipy_recon_config.mapmri": false, + "dipy_recon_config.laplacian_weighting": 0.05, + "dipy_recon_config.shore_positive_constraint": true, + "diffusion_imaging_model": "DSI", + "processing_tool_editor": ["Dipy", "MRtrix", "Custom"] + }, + + + "preprocessing_stage": { + "eddy_current_and_motion_correction": true, + "description": "description", + "denoising": true, + "total_readout": 0.0, + "eddy_correct_motion_correction": true, + "dipy_noise_model": "Rician", + "denoising_algo": "MRtrix [MP-PCA]", + "bias_field_algo": "ANTS N4", + "bias_field_correction": true, + "fast_use_priors": true, + "resampling": [3, 3, 3], + "partial_volume_estimation": true, + "eddy_correction_algo": "FSL eddy_correct", + "interpolation": "interpolate" + }, + +"connectome_stage": { + "circular_layout": false, + "output_types": ["gpickle", "mat", "graphml"], + "compute_curvature": true, + "log_visualization": true, + "connectivity_metrics": ["Fiber number", "Fiber length", "Fiber density", "Fiber proportion", "Normalized fiber density" , "ADC", "gFA"] + }, + +"registration_stage": { + "pipeline": "Diffusion", + "registration_mode": "FSL [Linear]", + "use_float_precision": false, + "ants_interpolation": "BSpline", + "ants_bspline_interpolation_parameters": [3], + "ants_gauss_interpolation_parameters": [5.0, 5.0], + "ants_multilab_interpolation_parameters": [5.0, 5.0], + "ants_lower_quantile": 0.005, + "ants_upper_quantile": 0.995, + "ants_convergence_thresh": 1e-06, + "ants_convergence_winsize": 10, + "ants_linear_gradient_step": 0.1, + "ants_linear_cost": "MI", + "ants_linear_sampling_perc": 0.25, + "ants_linear_sampling_strategy": "Regular", + "ants_perform_syn": true, + "ants_nonlinear_gradient_step": 0.1, + "ants_nonlinear_cost": "CC", + "ants_nonlinear_update_field_variance": 3.0, + "ants_nonlinear_total_field_variance": 0.0, + "uses_qform": true, + "dof": 6, + "fsl_cost": "normmi", + "no_search": true, + "init": "header", + "contrast_type": "dti", + "apply_to_eroded_wm": true, + "apply_to_eroded_csf": true, + "apply_to_eroded_brain": false + }, + +"Multi-processing": { + "number_of_cores": 1 + } + + + +} \ No newline at end of file diff --git a/.circleci/tests/configuration_files/ref_diffusion_config_3.json b/.circleci/tests/configuration_files/ref_diffusion_config_3.json new file mode 100644 index 00000000..bc84424b --- /dev/null +++ b/.circleci/tests/configuration_files/ref_diffusion_config_3.json @@ -0,0 +1,142 @@ + +{ + "Global": { + "process_type": "diffusion", + "subject_session": "ses-01", + "diffusion_imaging_model": "DSI", + "dmri_bids_acq": "DSI", + "subjects": ["sub-01"], + "subject": "sub-01" + }, + +"diffusion_stage": { + "tracking_processing_tool_editor": ["Dipy", "MRtrix", "Custom"], + "tracking_processing_tool": "Dipy", + "dilation_kernel": "Box", + "recon_processing_tool_editor": ["Dipy", "Custom"], + "dilation_radius": 1, + "diffusion_model": "Deterministic", + "dilate_rois": true, + "recon_processing_tool": "Dipy", + "dipy_tracking_config.fa_thresh": 0.2, + "dipy_tracking_config.seed_density": 1.0, + "dipy_tracking_config.number_of_seeds": 1000, + "dipy_tracking_config.tracking_mode": "Deterministic", + "dipy_tracking_config.use_act": false, + "dipy_tracking_config.imaging_model": "DSI", + "dipy_tracking_config.sh_order": 8, + "dipy_tracking_config.curvature": 0.0, + "dipy_tracking_config.step_size": 0.5, + "dipy_tracking_config.seed_from_gmwmi": false, + "dipy_tracking_config.sd": true, + "dipy_tracking_config.max_angle": 25.0, + "diffusion_imaging_model_editor": ["DSI", "DTI", "HARDI"], + "mrtrix_tracking_config.min_length": 5, + "mrtrix_tracking_config.angle": 45, + "mrtrix_tracking_config.tracking_mode": "Deterministic", + "mrtrix_tracking_config.use_act": true, + "mrtrix_tracking_config.cutoff_value": 0.05, + "mrtrix_tracking_config.backtrack": false, + "mrtrix_tracking_config.curvature": 0.0, + "mrtrix_tracking_config.crop_at_gmwmi": true, + "mrtrix_tracking_config.step_size": 0.5, + "mrtrix_tracking_config.max_length": 500, + "mrtrix_tracking_config.desired_number_of_tracks": 200000, + "mrtrix_tracking_config.seed_from_gmwmi": false, + "mrtrix_tracking_config.sd": true, + "mrtrix_recon_config.recon_mode": "Probabilistic", + "mrtrix_recon_config.imaging_model": "DSI", + "mrtrix_recon_config.single_fib_thr": 0.7, + "mrtrix_recon_config.lmax_order": "Auto", + "mrtrix_recon_config.local_model_editor": {"true": "Constrained Spherical Deconvolution"}, + "mrtrix_recon_config.local_model": true, + "mrtrix_recon_config.normalize_to_b0": false, + "diffusion_model_editor": ["Deterministic", "Probabilistic"], + "dipy_recon_config.shore_radial_order": 4, + "dipy_recon_config.shore_constrain_e0": false, + "dipy_recon_config.positivity_constraint": true, + "dipy_recon_config.tracking_processing_tool": "MRtrix", + "dipy_recon_config.imaging_model": "DSI", + "dipy_recon_config.small_delta": 0.02, + "dipy_recon_config.big_delta": 0.5, + "dipy_recon_config.lmax_order": "Auto", + "dipy_recon_config.shore_lambdal": 1e-08, + "dipy_recon_config.shore_lambdan": 1e-08, + "dipy_recon_config.local_model_editor": {"false": "1:Tensor", "true": "2:Constrained Spherical Deconvolution "}, + "dipy_recon_config.shore_zeta": 700, + "dipy_recon_config.local_model": true, + "dipy_recon_config.radial_order": 8, + "dipy_recon_config.radial_order_values": [2, 4, 6, 8, 10, 12], + "dipy_recon_config.single_fib_thr": 0.7, + "dipy_recon_config.recon_mode": "Probabilistic", + "dipy_recon_config.shore_tau": 0.0441759, + "dipy_recon_config.laplacian_regularization": true, + "dipy_recon_config.mapmri": false, + "dipy_recon_config.laplacian_weighting": 0.05, + "dipy_recon_config.shore_positive_constraint": true, + "diffusion_imaging_model": "DSI", + "processing_tool_editor": ["Dipy", "MRtrix", "Custom"] + }, + +"preprocessing_stage": { + "eddy_current_and_motion_correction": true, + "description": "description", + "denoising": true, + "total_readout": 0.0, + "eddy_correct_motion_correction": true, + "dipy_noise_model": "Rician", + "denoising_algo": "MRtrix [MP-PCA]", + "bias_field_algo": "ANTS N4", + "bias_field_correction": true, + "fast_use_priors": true, + "resampling": [3, 3, 3], + "partial_volume_estimation": true, + "eddy_correction_algo": "FSL eddy_correct", + "interpolation": "interpolate" + }, + +"connectome_stage": { + "circular_layout": false, + "output_types": ["gpickle"], + "compute_curvature": false, + "log_visualization": true, + "connectivity_metrics": ["Fiber number", "Fiber length", "Fiber density", "Fiber proportion", "Normalized fiber density" , "ADC", "gFA"] + }, + +"registration_stage": { + "ants_convergence_winsize" : 10, + "ants_nonlinear_update_field_variance" : 3.0, + "contrast_type" : "dti", + "ants_upper_quantile" : 0.995, + "use_float_precision" : false, + "ants_nonlinear_total_field_variance" : 0.0, + "registration_mode" : "ANTs", + "init" : "header", + "ants_interpolation" : "BSpline", + "ants_linear_sampling_perc" : 0.25, + "apply_to_eroded_wm" : true, + "ants_convergence_thresh" : 1e-06, + "ants_multilab_interpolation_parameters" : [5, 5], + "ants_gauss_interpolation_parameters" : [5, 5], + "ants_nonlinear_cost" : "CC", + "ants_bspline_interpolation_parameters" : [3], + "apply_to_eroded_brain" : false, + "uses_qform" : true, + "pipeline" : "Diffusion", + "ants_lower_quantile" : 0.005, + "no_search" : true, + "ants_linear_cost" : "MI", + "ants_linear_gradient_step" : 0.1, + "apply_to_eroded_csf" : true, + "ants_perform_syn" : true, + "ants_linear_sampling_strategy" : "Regular", + "dof" : 6, + "fsl_cost" : "normmi", + "ants_nonlinear_gradient_step" : 0.1 + + }, + + "Multi-processing": { + "number_of_cores" : 1 + } +} diff --git a/.circleci/tests/configuration_files/ref_diffusion_config_4.json b/.circleci/tests/configuration_files/ref_diffusion_config_4.json new file mode 100644 index 00000000..9f3a3390 --- /dev/null +++ b/.circleci/tests/configuration_files/ref_diffusion_config_4.json @@ -0,0 +1,142 @@ +{ + "Global": { + "process_type": "diffusion", + "subject_session": "ses-01", + "diffusion_imaging_model": "DSI", + "dmri_bids_acq": "DSI", + "subjects": ["sub-01"], + "subject": "sub-01" + }, + + "diffusion_stage": { + "tracking_processing_tool_editor": ["Dipy", "MRtrix", "Custom"], + "tracking_processing_tool": "Dipy", + "dilation_kernel": "Box", + "recon_processing_tool_editor": ["Dipy", "Custom"], + "dilation_radius": 1, + "diffusion_model": "Probabilistic", + "dilate_rois": true, + "recon_processing_tool": "Dipy", + "dipy_tracking_config.fa_thresh": 0.2, + "dipy_tracking_config.seed_density": 1.0, + "dipy_tracking_config.number_of_seeds": 1000, + "dipy_tracking_config.tracking_mode": "Probabilistic", + "dipy_tracking_config.use_act": true, + "dipy_tracking_config.imaging_model": "DSI", + "dipy_tracking_config.sh_order": 8, + "dipy_tracking_config.curvature": 0.0, + "dipy_tracking_config.step_size": 0.5, + "dipy_tracking_config.seed_from_gmwmi": false, + "dipy_tracking_config.sd": true, + "dipy_tracking_config.max_angle": 25.0, + "diffusion_imaging_model_editor": ["DSI", "DTI", "HARDI"], + "mrtrix_tracking_config.min_length": 5, + "mrtrix_tracking_config.angle": 45, + "mrtrix_tracking_config.tracking_mode": "Deterministic", + "mrtrix_tracking_config.use_act": true, + "mrtrix_tracking_config.cutoff_value": 0.05, + "mrtrix_tracking_config.backtrack": false, + "mrtrix_tracking_config.curvature": 0.0, + "mrtrix_tracking_config.crop_at_gmwmi": true, + "mrtrix_tracking_config.step_size": 0.5, + "mrtrix_tracking_config.max_length": 500, + "mrtrix_tracking_config.desired_number_of_tracks": 200000, + "mrtrix_tracking_config.seed_from_gmwmi": false, + "mrtrix_tracking_config.sd": true, + "mrtrix_recon_config.recon_mode": "Probabilistic", + "mrtrix_recon_config.imaging_model": "DSI", + "mrtrix_recon_config.single_fib_thr": 0.7, + "mrtrix_recon_config.lmax_order": "Auto", + "mrtrix_recon_config.local_model_editor": {"true": "Constrained Spherical Deconvolution"}, + "mrtrix_recon_config.local_model": true, + "mrtrix_recon_config.normalize_to_b0": false, + "diffusion_model_editor": ["Deterministic", "Probabilistic"], + "dipy_recon_config.shore_radial_order": 4, + "dipy_recon_config.shore_constrain_e0": false, + "dipy_recon_config.positivity_constraint": true, + "dipy_recon_config.tracking_processing_tool": "MRtrix", + "dipy_recon_config.imaging_model": "DSI", + "dipy_recon_config.small_delta": 0.02, + "dipy_recon_config.big_delta": 0.5, + "dipy_recon_config.lmax_order": "Auto", + "dipy_recon_config.shore_lambdal": 1e-08, + "dipy_recon_config.shore_lambdan": 1e-08, + "dipy_recon_config.local_model_editor": {"false": "1:Tensor", "true": "2:Constrained Spherical Deconvolution "}, + "dipy_recon_config.shore_zeta": 700, + "dipy_recon_config.local_model": true, + "dipy_recon_config.radial_order": 8, + "dipy_recon_config.radial_order_values": [2, 4, 6, 8, 10, 12], + "dipy_recon_config.single_fib_thr": 0.7, + "dipy_recon_config.recon_mode": "Probabilistic", + "dipy_recon_config.shore_tau": 0.0441759, + "dipy_recon_config.laplacian_regularization": true, + "dipy_recon_config.mapmri": false, + "dipy_recon_config.laplacian_weighting": 0.05, + "dipy_recon_config.shore_positive_constraint": true, + "diffusion_imaging_model": "DSI", + "processing_tool_editor": ["Dipy", "MRtrix", "Custom"] + }, + + "preprocessing_stage": { + "eddy_current_and_motion_correction": true, + "description": "description", + "denoising": true, + "total_readout": 0.0, + "eddy_correct_motion_correction": true, + "dipy_noise_model": "Rician", + "denoising_algo": "MRtrix [MP-PCA]", + "bias_field_algo": "ANTS N4", + "bias_field_correction": true, + "fast_use_priors": true, + "resampling": [3, 3, 3], + "partial_volume_estimation": true, + "eddy_correction_algo": "FSL eddy_correct", + "interpolation": "interpolate" + }, + + "connectome_stage": { + "circular_layout": false, + "output_types": ["gpickle"], + "compute_curvature": false, + "log_visualization": true, + "connectivity_metrics": ["Fiber number", "Fiber length", "Fiber density", "Fiber proportion", "Normalized fiber density" , "ADC", "gFA"] + }, + + "registration_stage": { + "ants_convergence_winsize" : 10, + "ants_nonlinear_update_field_variance" : 3.0, + "contrast_type" : "dti", + "ants_upper_quantile" : 0.995, + "use_float_precision" : false, + "ants_nonlinear_total_field_variance" : 0.0, + "registration_mode" : "ANTs", + "init" : "header", + "ants_interpolation" : "BSpline", + "ants_linear_sampling_perc" : 0.25, + "apply_to_eroded_wm" : true, + "ants_convergence_thresh" : 1e-06, + "ants_multilab_interpolation_parameters" : [5, 5], + "ants_gauss_interpolation_parameters" : [5, 5], + "ants_nonlinear_cost" : "CC", + "ants_bspline_interpolation_parameters" : [3], + "apply_to_eroded_brain" : false, + "uses_qform" : true, + "pipeline" : "Diffusion", + "ants_lower_quantile" : 0.005, + "no_search" : true, + "ants_linear_cost" : "MI", + "ants_linear_gradient_step" : 0.1, + "apply_to_eroded_csf" : true, + "ants_perform_syn" : true, + "ants_linear_sampling_strategy" : "Regular", + "dof" : 6, + "fsl_cost" : "normmi", + "ants_nonlinear_gradient_step" : 0.1 + + }, + + "Multi-processing": { + "number_of_cores" : 1 + } +} + diff --git a/.circleci/tests/configuration_files/ref_diffusion_config_5.json b/.circleci/tests/configuration_files/ref_diffusion_config_5.json new file mode 100644 index 00000000..3cb743b3 --- /dev/null +++ b/.circleci/tests/configuration_files/ref_diffusion_config_5.json @@ -0,0 +1,137 @@ +{ + "Global": { + "process_type": "diffusion", + "diffusion_imaging_model": "DSI", + "subjects": ["sub-01"], + "subject": "sub-01", + "subject_session": "ses-01", + "dmri_bids_acq": "DSI" + }, + + "preprocessing_stage": { + "total_readout": 0.0, + "description": "description", + "denoising": true, + "denoising_algo": "MRtrix [MP-PCA]", + "dipy_noise_model": "Rician", + "bias_field_correction": true, + "bias_field_algo": "ANTS N4", + "eddy_current_and_motion_correction": true, + "eddy_correction_algo": "FSL eddy_correct", + "partial_volume_estimation": true, + "fast_use_priors": true, + "resampling": [3, 3, 3], + "interpolation": "interpolate" + }, + + + "registration_stage": { + "pipeline" : "Diffusion", + "registration_mode": "FSL", + "use_float_precision": false, + "ants_interpolation" : "BSpline", + "ants_bspline_interpolation_parameters" : [3], + "ants_gauss_interpolation_parameters" : [5, 5], + "ants_multilab_interpolation_parameters" : [5, 5], + "ants_lower_quantile" : 0.005, + "ants_upper_quantile" : 0.995, + "ants_convergence_thresh": 1e-06, + "ants_convergence_winsize" : 10, + "ants_linear_gradient_step" : 0.1, + "ants_nonlinear_cost" : "CC", + "ants_nonlinear_update_field_variance" : 3.0, + "ants_nonlinear_total_field_variance" : 0.0, + "uses_qform" : true, + "dof" : 6, + "fsl_cost" : "normmi", + "no_search" : true, + "init" : "header", + "contrast_type" : "dti", + "apply_to_eroded_wm" : true, + "apply_to_eroded_csf" : true, + "apply_to_eroded_brain" : false + }, + + + "diffusion_stage": { + "tracking_processing_tool_editor": ["Dipy", "MRtrix", "Custom"], + "diffusion_imaging_model" : "DSI", + "dilate_rois": true, + "dilation_kernel": "Box", + "dilation_radius": 1, + "recon_processing_tool_editor": ["Dipy", "Custom"], + "processing_tool_editor": ["Dipy", "MRtrix", "Custom"], + "recon_processing_tool": "Dipy", + "tracking_processing_tool": "MRtrix", + "dipy_recon_config.imaging_model": "DSI", + "dipy_recon_config.local_model": true, + "dipy_recon_config.lmax_order": "Auto", + "dipy_recon_config.single_fib_thr": 0.7, + "dipy_recon_config.recon_mode": "Probabilistic", + "dipy_recon_config.mapmri": false, + "dipy_recon_config.tracking_processing_tool": "MRtrix", + "dipy_recon_config.laplacian_regularization": false, + "dipy_recon_config.laplacian_weighting": 0.05, + "dipy_recon_config.positivity_constraint": true, + "dipy_recon_config.shore_radial_order": 4, + "dipy_recon_config.small_delta": 0.02, + "dipy_recon_config.big_delta": 0.5, + "dipy_recon_config.radial_order_values": [2, 4, 6, 8, 10, 12], + "dipy_recon_config.radial_order": 4, + "dipy_recon_config.shore_zeta": 700, + "dipy_recon_config.shore_lambda_l": 1e-08, + "dipy_recon_config.shore_lambda_n": 1e-08, + "dipy_recon_config.shore_tau": 0.0441759, + "dipy_recon_config.shore_constrain_e0": false, + "dipy_recon_config.shore_positive_constraint": true, + "dipy_recon_config.local_model_editor": {"false": "1:Tensor", "true": "2:Constrained Spherical Deconvolution "}, + "mrtrix_recon_config.local_model_editor": {"true": "Constrained Spherical Deconvolution"}, + "mrtrix_recon_config.local_model": true, + "mrtrix_recon_config.lmax_order": 2, + "mrtrix_recon_config.normalize_to_b0": false, + "mrtrix_recon_config.single_fib_thr": 0.7, + "mrtrix_recon_config.recon_mode": "Probabilistic", + "mrtrix_recon_config.imaging_model": "DSI", + "dipy_tracking_config.imaging_model": "DSI", + "dipy_tracking_config.tracking_mode": "Deterministic", + "dipy_tracking_config.sd": true, + "dipy_tracking_config.number_of_seeds": 1000, + "dipy_tracking_config.seed_density": 1.0, + "dipy_tracking_config.fa_thresh": 0.2, + "dipy_tracking_config.step_size": 0.5, + "dipy_tracking_config.max_angle": 25.0, + "dipy_tracking_config.sh_order": 8, + "dipy_tracking_config.use_act": false, + "dipy_tracking_config.seed_from_gmwmi": false, + "dipy_tracking_config.curvature": 0.0, + "mrtrix_tracking_config.tracking_mode": "Deterministic", + "mrtrix_tracking_config.sd": true, + "mrtrix_tracking_config.desired_number_of_tracks": 200000, + "mrtrix_tracking_config.curvature": 0.0, + "mrtrix_tracking_config.step_size": 0.5, + "mrtrix_tracking_config.min_length": 5, + "mrtrix_tracking_config.max_length": 200, + "mrtrix_tracking_config.angle": 45, + "mrtrix_tracking_config.cutoff_value": 0.05, + "mrtrix_tracking_config.use_act": true, + "mrtrix_tracking_config.seed_from_gmwmi": false, + "mrtrix_tracking_config.crop_at_gmwmi": false, + "mrtrix_tracking_config.backtrack": false, + "mrtrix_tracking_config.sift": true, + "diffusion_model_editor": ["Deterministic", "Probabilistic"], + "diffusion_model": "Deterministic" + }, + + "connectome_stage": { + "output_types": ["gpickle"], + "connectivity_metrics": ["Fiber number", "Fiber length", "Fiber density", "Fiber proportion", "Normalized fiber density" , "ADC", "gFA"], + "compute_curvature": false, + "log_visualization": true, + "circular_layout": false + }, + + + "Multi-processing": { + "number_of_cores" : 1 + } +} diff --git a/.circleci/tests/configuration_files/ref_fMRI_config_1.nii.json b/.circleci/tests/configuration_files/ref_fMRI_config_1.nii.json new file mode 100644 index 00000000..8ed986f7 --- /dev/null +++ b/.circleci/tests/configuration_files/ref_fMRI_config_1.nii.json @@ -0,0 +1,81 @@ +{ + "Global": { + "process_type": "fMRI", + "subjects": ["sub-01"], + "subject": "sub-01", + "subject_session": "ses-01" + }, + + "preprocessing_stage": { + "discard_n_volumes": 5, + "despiking": true, + "slice_timing": "bottom-top interleaved", + "repetition_time": 0.5, + "motion_correction": true + }, + + "registration_stage": { + "pipeline": "fMRI", + "registration_mode" : "BBregister (FS)", + "use_float_precision" : false, + "ants_interpolation" : "Linear", + "ants_bspline_interpolation_parameters" : [3], + "ants_gauss_interpolation_parameters" : [5, 5], + "ants_multilab_interpolation_parameters" : [5, 5], + "ants_lower_quantile" : 0.005, + "ants_upper_quantile" : 0.995, + "ants_convergence_thresh" : 1e-06, + "ants_convergence_winsize" : 10, + "ants_linear_gradient_step" : 0.1, + "ants_linear_cost" : "MI", + "ants_linear_sampling_perc" : 0.25, + "ants_linear_sampling_strategy" : "Regular", + "ants_perform_syn" : true, + "ants_nonlinear_gradient_step" : 0.1, + "ants_nonlinear_cost" : "CC", + "ants_nonlinear_update_field_variance" : 3.0, + "ants_nonlinear_total_field_variance" : 0.0, + "uses_qform" : true, + "dof" : 6, + "fsl_cost" : "normmi", + "no_search" : true, + "init" : "header", + "contrast_type" : "t2", + "apply_to_eroded_wm" : true, + "apply_to_eroded_csf" : true, + "apply_to_eroded_brain" : false + }, + + "functional_stage":{ + "smoothing" : 0.0, + "discard_n_volumes" : 5, + "global_nuisance" : false, + "csf" : true, + "wm" : true, + "motion" : true, + "detrending" : true, + "detrending_mode" : "quadratic", + "perform_filtering" : true, + "lowpass_filter" : 0.01, + "highpass_filter" : 0.1, + "scrubbing" : true + }, + + "connectome_stage": { + "output_types" : ["gpickle", "mat", "graphml"], + "apply_scrubbing" : false, + "fd_thr" : 0.2, + "dvars_thr" : 4.0, + "log_visualization" : true, + "circular_layout" : false, + "subject" : "sub-01" + }, + + + "Multi-processing": { + "number_of_cores" : 1 + } + + + +} diff --git a/.circleci/tests/configuration_files/ref_fMRI_config_2.json b/.circleci/tests/configuration_files/ref_fMRI_config_2.json new file mode 100644 index 00000000..1555e84c --- /dev/null +++ b/.circleci/tests/configuration_files/ref_fMRI_config_2.json @@ -0,0 +1,81 @@ +{ + "Global": { + "process_type": "fMRI", + "subjects": ["sub-01"], + "subject": "sub-01", + "subject_session": "ses-01" + }, + + "preprocessing_stage": { + "discard_n_volumes": 5, + "despiking": true, + "slice_timing": "bottom-top interleaved", + "repetition_time": 0.5, + "motion_correction": true + }, + + "registration_stage": { + "ants_convergence_winsize" : 10, + "ants_nonlinear_update_field_variance" : 3.0, + "contrast_type" : "dti", + "ants_upper_quantile" : 0.995, + "use_float_precision" : false, + "ants_nonlinear_total_field_variance" : 0.0, + "registration_mode" : "FSL (Linear)", + "init" : "header", + "ants_interpolation" : "Linear", + "ants_linear_sampling_perc" : 0.25, + "apply_to_eroded_wm" : true, + "ants_convergence_thresh" : 1e-06, + "ants_multilab_interpolation_parameters" : [5, 5], + "ants_gauss_interpolation_parameters" : [5, 5], + "ants_nonlinear_cost" : "CC", + "ants_bspline_interpolation_parameters" : [3], + "apply_to_eroded_brain" : false, + "uses_qform" : true, + "pipeline": "fMRI", + "ants_lower_quantile" : 0.005, + "no_search" : true, + "ants_linear_cost" : "MI", + "ants_linear_gradient_step" : 0.1, + "apply_to_eroded_csf" : true, + "ants_perform_syn" : true, + "ants_linear_sampling_strategy" : "Regular", + "dof" : 6, + "fsl_cost" : "normmi", + "ants_nonlinear_gradient_step" : 0.1 + }, + + "functional_stage":{ + "smoothing" : 0.0, + "discard_n_volumes" : 5, + "global_nuisance" : true, + "csf" : true, + "wm" : true, + "motion" : true, + "detrending" : true, + "detrending_mode" : "linear", + "perform_filtering" : false, + "lowpass_filter" : 0.01, + "highpass_filter" : 0.1, + "scrubbing" : true + }, + + "connectome_stage": { + "output_types" : ["gpickle", "mat"], + "apply_scrubbing" : true, + "fd_thr" : 0.2, + "dvars_thr" : 4.0, + "log_visualization" : true, + "circular_layout" : false, + "subject" : "sub-01" + }, + + + "Multi-processing": { + "number_of_cores" : 1 + } + + + +} \ No newline at end of file From d476999af2a9dd95f4ff5d9e000fa6142b61cd6e Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 13 Aug 2024 09:47:33 +0200 Subject: [PATCH 05/26] [upd] Update test outputs for test1 and test2 --- .../ds-sample_test-01_outputs.txt | 7 +- .../ds-sample_test-02_outputs.txt | 257 ++++++++++-------- 2 files changed, 147 insertions(+), 117 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt index 2d71d41d..237d0e1d 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt @@ -37,12 +37,8 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_fMRI_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt -freesurfer-7.1.1/dataset_description (copy 1).json freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -150,6 +146,7 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -169,6 +166,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -189,6 +187,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz diff --git a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt index 37a6dcaa..680b3c99 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt @@ -1,29 +1,32 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json +cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab -freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz -freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab +freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.label @@ -44,20 +47,35 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label 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nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/fsmask_1mm.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/gmmask.nii.gz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_report/report.rst nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/result_NativeFreesurfer_parcellation.pklz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/ribbon.nii.gz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/ROIv_HR_th_freesurferaparc.nii.gz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/T1.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/wm_eroded.nii.gz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/_node.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/_report/report.rst -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/freesurferaparc_roi_stats.tsv -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/compute_roi_volumetry/result_compute_roi_volumetry.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_node.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/_report/report.rst -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/createBIDSLabelIndexMappingFile/result_createBIDSLabelIndexMappingFile.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log \ No newline at end of file From 14596d74eb3fcf97addf37f7732caf08929cdff0 Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 13 Aug 2024 10:00:54 +0200 Subject: [PATCH 06/26] [upd] Update from datalad 0.17.2 to 0.17.3 --- docker/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/requirements.txt b/docker/requirements.txt index ddf6a9ba..a9a5f399 100644 --- a/docker/requirements.txt +++ b/docker/requirements.txt @@ -4,7 +4,7 @@ duecredit==0.8.0 nibabel==3.2.2 mne==0.24.1 mne_connectivity==0.3 -datalad[full]==0.17.2 +datalad[full]==0.17.3 datalad-container==1.1.6 datalad-neuroimaging==0.3.1 pybids==0.14.0 From 03c27268057aead4e4cdf6d28660c6ee58176547 Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 13 Aug 2024 10:15:41 +0200 Subject: [PATCH 07/26] [upd] update test04 --- .../ds-sample_test-04_outputs.txt | 69 ++++++++++++++++--- 1 file changed, 58 insertions(+), 11 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt index 86b26a71..5bc7dabe 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt @@ -46,19 +46,27 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GMWMI_probseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale3_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale4_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale5_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-CSF_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval @@ -74,11 +82,9 @@ cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_fMRI_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt cmp-v3.2.0/sub-01/ses-01/xfm/final0GenericAffine.mat cmp-v3.2.0/sub-01/ses-01/xfm/final1Warp.nii.gz -freesurfer-7.1.1/dataset_description (copy 1).json freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -186,6 +192,7 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -205,6 +212,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -225,6 +233,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz @@ -526,10 +535,25 @@ nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/R nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3_dil.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale1.gpickle +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale1.graphml +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale1.mat nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale1.tsv +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale2.gpickle +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale2.graphml +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale2.mat nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale2.tsv +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale3.gpickle +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale3.graphml +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale3.mat nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale3.tsv +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale4.gpickle +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale4.graphml +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale4.mat nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale4.tsv +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale5.gpickle +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale5.graphml +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale5.mat nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale5.tsv nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/endpointsmm.npy nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/endpoints.npy @@ -723,6 +747,12 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask_ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask_pre/result_flirt_dwimask_pre.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/flirt_dwimask/result_flirt_dwimask.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/gmwmi_resample/command.txt +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/gmwmi_resample/gmwmi_resampled.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/gmwmi_resample/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/gmwmi_resample/_node.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/gmwmi_resample/_report/report.rst +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/gmwmi_resample/result_gmwmi_resample.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/indexnode/index.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/indexnode/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/indexnode/_node.pklz @@ -944,10 +974,21 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/mrt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/result_mrtrix_5tt.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_gmwmi/command.txt +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_gmwmi/gmwmi.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_gmwmi/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_gmwmi/_node.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_gmwmi/_report/report.rst +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_gmwmi/result_mrtrix_gmwmi.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/ROIs_resample/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/ROIs_resample/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/ROIs_resample/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/ROIs_resample/result_ROIs_resample.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/update_gmwmi/gmwmi_proc.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/update_gmwmi/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/update_gmwmi/_node.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/update_gmwmi/_report/report.rst +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/update_gmwmi/result_update_gmwmi.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/_node.pklz @@ -973,6 +1014,12 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_brai nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_brain/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_brain/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_brain/result_apply_warp_brain.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_gmwmi/command.txt +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_gmwmi/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_gmwmi/_node.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_gmwmi/_report/report.rst +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_gmwmi/result_apply_warp_gmwmi.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/_report/report.rst @@ -1088,4 +1135,4 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmas nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/result_tensor2FA_unmasked.pklz \ No newline at end of file +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/result_tensor2FA_unmasked.pklz From 64d67785adf10add423a847ba5a314a5104c44b1 Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 13 Aug 2024 10:18:02 +0200 Subject: [PATCH 08/26] [upd] Update from datalad 0.17.3 to 0.19.2 --- docker/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/requirements.txt b/docker/requirements.txt index a9a5f399..5ea8edc9 100644 --- a/docker/requirements.txt +++ b/docker/requirements.txt @@ -4,7 +4,7 @@ duecredit==0.8.0 nibabel==3.2.2 mne==0.24.1 mne_connectivity==0.3 -datalad[full]==0.17.3 +datalad[full]==0.19.2 datalad-container==1.1.6 datalad-neuroimaging==0.3.1 pybids==0.14.0 From 894fc72fb8422f78f5c460bf18101f66f3d789a1 Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 13 Aug 2024 10:58:35 +0200 Subject: [PATCH 09/26] [upd] update test06 --- .../ds-sample_test-06_outputs.txt | 78 ++++++++++++------- 1 file changed, 51 insertions(+), 27 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt index ab8eaa55..8b7eefc4 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt @@ -74,6 +74,7 @@ cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json +cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt cmp-v3.2.0/sub-01/ses-01/xfm/final0GenericAffine.mat cmp-v3.2.0/sub-01/ses-01/xfm/final1Warp.nii.gz freesurfer-7.1.1/dataset_description.json @@ -105,14 +106,24 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label @@ -144,14 +155,24 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label @@ -160,9 +181,10 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -182,6 +204,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -190,6 +213,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log.bak freesurfer-7.1.1/sub-01_ses-01/mri/norm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/nu.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/orig/001.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig_nu.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz @@ -201,6 +225,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz @@ -212,6 +237,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/segment.dat +freesurfer-7.1.1/sub-01_ses-01/mri/surface.defects.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/talairach.label_intensities.txt @@ -226,12 +252,14 @@ freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm +freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt +freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log @@ -243,7 +271,10 @@ freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.local-copy freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.log freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log +freesurfer-7.1.1/sub-01_ses-01/scripts/recon-config.yaml +freesurfer-7.1.1/sub-01_ses-01/scripts/unknown-args.txt freesurfer-7.1.1/sub-01_ses-01/stats/aseg.stats +freesurfer-7.1.1/sub-01_ses-01/stats/brainvol.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.a2009s.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.pial.stats @@ -261,6 +292,8 @@ freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats +freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat +freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -270,6 +303,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels +freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -277,7 +311,8 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial +freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.premesh +freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial.T1 freesurfer-7.1.1/sub-01_ses-01/surf/lh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.BE.crv @@ -308,6 +343,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_labels +freesurfer-7.1.1/sub-01_ses-01/surf/rh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.K @@ -315,7 +351,8 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial +freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.premesh +freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial.T1 freesurfer-7.1.1/sub-01_ses-01/surf/rh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm.BE.crv @@ -345,8 +382,6 @@ freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/touch/aparc.a2009s2aseg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/aparc.DKTatlas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/apas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/asegmerge.touch freesurfer-7.1.1/sub-01_ses-01/touch/ca_label.touch @@ -363,25 +398,26 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.curvstats.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.pctsurfcon.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.pial_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.qsphere.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphmorph.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphreg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.surfvolume.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.tessellate.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.topofix.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.H.K.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white_surface.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.preaparc.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.touch freesurfer-7.1.1/sub-01_ses-01/touch/nu.touch freesurfer-7.1.1/sub-01_ses-01/touch/relabelhypos.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc2.touch @@ -389,43 +425,31 @@ freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.avgcurv.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex+hipamyg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.curvstats.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.pctsurfcon.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.pial_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.qsphere.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.smoothwm1.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.smoothwm2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.sphmorph.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.sphreg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.surfvolume.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.tessellate.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.topofix.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.white.H.K.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.white_surface.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_ca_register.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_em_register.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_em_register.skull.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_fix_topology.lh.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_fix_topology.rh.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_inflate.lh.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_inflate.rh.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_register.lh.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_register.rh.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_sphere.lh.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_sphere.rh.dat -freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_watershed.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rh.white.preaparc.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.white.touch freesurfer-7.1.1/sub-01_ses-01/touch/segstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/skull.lta.touch freesurfer-7.1.1/sub-01_ses-01/touch/skull_strip.touch freesurfer-7.1.1/sub-01_ses-01/touch/talairach.touch freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.stats.touch -freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.touch freesurfer-7.1.1/sub-01_ses-01/touch/wmsegment.touch nipype-1.8.0/dataset_description.json nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/_inputs.pklz @@ -1066,4 +1090,4 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmas nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/result_tensor2FA_unmasked.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/result_tensor2FA_unmasked.pklz \ No newline at end of file From b490f4957c65dec86a89d89b987c931bd7de0872 Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 13 Aug 2024 11:12:54 +0200 Subject: [PATCH 10/26] [fix] Update test02 second test --- .../ds-sample_test-02_outputs.txt | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt index 680b3c99..769cbac0 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt @@ -17,7 +17,6 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -47,18 +46,9 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot @@ -100,14 +90,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot From 7b54c1c87e08298bed21585c48f11f54acfa469e Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 13 Aug 2024 12:01:45 +0200 Subject: [PATCH 11/26] [upd] update test01 and test02 --- .../ds-sample_test-01_outputs.txt | 17 ----------------- .../ds-sample_test-02_outputs.txt | 11 ----------- 2 files changed, 28 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt index 237d0e1d..21d96a30 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt @@ -38,7 +38,6 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -72,14 +71,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot @@ -121,14 +112,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot diff --git a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt index 769cbac0..6cb36d92 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt @@ -49,11 +49,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label @@ -90,11 +85,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label @@ -323,7 +313,6 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.curvstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate1.touch From d4107d7ba84856452605390846ed7c566c635896 Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 13 Aug 2024 12:05:03 +0200 Subject: [PATCH 12/26] [upd] update test07 and test08 --- .../ds-sample_test-07_outputs.txt | 428 +++++++++--------- .../ds-sample_test-08_outputs.txt | 408 +++++++++-------- 2 files changed, 442 insertions(+), 394 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt index 56272baa..4aefd6f6 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt @@ -1,42 +1,42 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale1_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale2_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale3_dseg.nii.gz @@ -82,13 +82,16 @@ cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.json cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_fMRI_config.json +cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab -freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz -freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab +freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.label @@ -109,25 +112,35 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA2_exvivo.label @@ -148,45 +161,37 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot 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-freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.S.crv +freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.K.crv freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.nofix +freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.S.crv freesurfer-7.1.1/sub-01_ses-01/surf/lh.sphere freesurfer-7.1.1/sub-01_ses-01/surf/lh.sphere.reg freesurfer-7.1.1/sub-01_ses-01/surf/lh.sulc @@ -314,6 +349,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_labels +freesurfer-7.1.1/sub-01_ses-01/surf/rh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.K @@ -321,18 +357,19 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig 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nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/_node.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/_report/report.rst -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/command.txt -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/eroded_wm_registered.nii.gz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/result_apply_registration_wm_eroded.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/sub-01_ses-01_label-WM_desc-eroded_dseg_flirt.mat -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/_node.pklz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/_report/report.rst +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm/_node.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm/_report/report.rst +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm/result_apply_registration_wm.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm/sub-01_ses-01_label-WM_dseg_flirt.mat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm/wm_mask_registered.nii.gz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/fMRI_despike_st_mcf.nii.gz_mean_reg_brain_bbreg_sub-01_ses-01.dat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/fMRI_despike_st_mcf.nii.gz_mean_reg_brain_bbreg_sub-01_ses-01.dat~ nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/fMRI_despike_st_mcf.nii.gz_mean_reg_brain_bbreg_sub-01_ses-01.dat.mincost nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/fMRI_despike_st_mcf.nii.gz_mean_reg_brain_bbreg_sub-01_ses-01.dat.param nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/fMRI_despike_st_mcf.nii.gz_mean_reg_brain_bbreg_sub-01_ses-01.dat.sum -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/fMRI_despike_st_mcf.nii.gz_mean_reg_brain_bbreg_sub-01_ses-01.dat~ nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/fMRI_despike_st_mcf.nii.gz_mean_reg_brain_bbreg_sub-01_ses-01.log +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/_node.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/_report/report.rst nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/result_bbregister.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/bbregister/target-TO-orig.mat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fMRI_skullstrip/command.txt +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fMRI_skullstrip/fMRI_despike_st_mcf.nii.gz_mean_reg_brain.nii.gz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fMRI_skullstrip/_inputs.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fMRI_skullstrip/_node.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fMRI_skullstrip/_report/report.rst -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fMRI_skullstrip/command.txt -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fMRI_skullstrip/fMRI_despike_st_mcf.nii.gz_mean_reg_brain.nii.gz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fMRI_skullstrip/result_fMRI_skullstrip.pklz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/T1-TO-orig.dat -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/T1-TO-orig.mat -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/_node.pklz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/_report/report.rst -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/command.txt -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/result_fs_tkregister2.pklz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_concatxfm/T1-TO-orig_target-TO-orig_inv.mat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_concatxfm/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_concatxfm/_inputs.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_concatxfm/_node.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_concatxfm/_report/report.rst -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_concatxfm/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_concatxfm/result_fsl_concatxfm.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_concatxfm/T1-TO-orig_target-TO-orig_inv.mat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_invertxfm/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_invertxfm/_inputs.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_invertxfm/_node.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_invertxfm/_report/report.rst -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_invertxfm/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_invertxfm/result_fsl_invertxfm.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fsl_invertxfm/target-TO-orig_inv.mat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/command.txt +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/_node.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/_report/report.rst +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/result_fs_tkregister2.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/T1-TO-orig.dat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/fs_tkregister2/T1-TO-orig.mat nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/get_fs_files/_inputs.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/get_fs_files/_node.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/get_fs_files/_report/report.rst nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/get_fs_files/result_get_fs_files.pklz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/linear_registration/T1-TO-TARGET.nii.gz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/linear_registration/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/linear_registration/_inputs.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/linear_registration/_node.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/linear_registration/_report/report.rst -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/linear_registration/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/linear_registration/result_linear_registration.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/linear_registration/sub-01_ses-01_desc-head_T1w_brain_flirt.mat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/linear_registration/T1-TO-TARGET.nii.gz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/command.txt +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/_node.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/_report/report.rst +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/result_T1_skullstrip.pklz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/sub-01_ses-01_desc-head_T1w_brain.nii.gz diff --git a/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt index 23649dd4..0081a84d 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt @@ -1,50 +1,50 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale1_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale2_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale3_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale4_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-brain_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-brain_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_label-WM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.mat @@ -78,13 +78,16 @@ cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.json cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_fMRI_config.json +cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab -freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz -freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab +freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.label @@ -105,25 +108,35 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label 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+freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA2_exvivo.label @@ -144,45 +157,37 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot 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+freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.mgz @@ -191,78 +196,106 @@ freesurfer-7.1.1/sub-01_ses-01/mri/aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.presurf.hypos.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.presurf.mgz freesurfer-7.1.1/sub-01_ses-01/mri/brain.finalsurfs.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/brain.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/brain.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/brainmask.auto.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/brainmask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/brainmask.mgz freesurfer-7.1.1/sub-01_ses-01/mri/brainmask.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/brainmask_eroded.nii.gz 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+nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/T1_skullstrip/sub-01_ses-01_desc-head_T1w_brain.nii.gz From b3bba97e64235e8cb6502a05a52f38b77a34298d Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 13 Aug 2024 16:58:27 +0200 Subject: [PATCH 13/26] [upd] update test circle from reprocessing local from scratch --- .../ds-sample_test-01_outputs.txt | 37 +- .../ds-sample_test-02_outputs.txt | 58 +- .../ds-sample_test-04_outputs.txt | 18 +- .../ds-sample_test-05_outputs.txt | 730 ++++++++---------- .../ds-sample_test-06_outputs.txt | 224 +----- .../ds-sample_test-07_outputs.txt | 236 +----- .../ds-sample_test-08_outputs.txt | 227 +----- 7 files changed, 510 insertions(+), 1020 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt index 21d96a30..c2679886 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt @@ -38,6 +38,7 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json +cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -71,6 +72,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot @@ -112,6 +121,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot @@ -129,7 +146,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -149,7 +165,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -170,7 +185,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz @@ -471,4 +485,19 @@ nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/R nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/ROIv_Lausanne2018_scale5.graphml nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3_dil.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3.nii.gz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log \ No newline at end of file +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/result_copyOrig.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/command.txt +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/result_mgzConvert.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/T1.mgz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/command.txt +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/result_reconall.pklz diff --git a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt index 6cb36d92..58b68fc2 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt @@ -17,6 +17,7 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json +cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -46,9 +47,18 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label @@ -85,6 +95,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label @@ -133,22 +151,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rh.ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/segment.dat freesurfer-7.1.1/sub-01_ses-01/mri/surface.defects.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz @@ -287,14 +290,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.white freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.K -freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.Lausanne2018.native.nii.gz -freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.native.nii.gz -freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale1_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/touch/apas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/asegmerge.touch freesurfer-7.1.1/sub-01_ses-01/touch/ca_label.touch @@ -313,6 +309,7 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.curvstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate1.touch @@ -403,4 +400,19 @@ nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurf nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/ROIv_HR_th_freesurferaparc.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/T1.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/wm_eroded.nii.gz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log \ No newline at end of file +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/result_copyOrig.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/command.txt +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/result_mgzConvert.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/T1.mgz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/command.txt +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/result_reconall.pklz diff --git a/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt index 5bc7dabe..730023c5 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt @@ -192,7 +192,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -212,7 +211,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -233,7 +231,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz @@ -535,6 +532,21 @@ nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/R nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3_dil.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/result_copyOrig.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/command.txt +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/result_mgzConvert.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/T1.mgz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/command.txt +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/result_reconall.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale1.gpickle nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale1.graphml nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/connectome_scale1.mat diff --git a/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt index e63e3cac..da374479 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt @@ -1,88 +1,37 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-CSF_probseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GM_probseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_probseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json -cmp-v3.2.0/sub-01/ses-01/xfm/final0GenericAffine.mat -cmp-v3.2.0/sub-01/ses-01/xfm/final1Warp.nii.gz +cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab -freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz -freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab +freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.label @@ -103,25 +52,30 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA2_exvivo.label @@ -142,45 +96,32 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label 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freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats +freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat +freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -270,6 +224,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels +freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -277,18 +232,19 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix 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nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/result_tensor2FA_unmasked.pklz diff --git a/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt index 8b7eefc4..2added49 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt @@ -1,31 +1,10 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml 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cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json @@ -37,46 +16,13 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz 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nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasource/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasource/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasource/_report/report.rst @@ -899,11 +763,7 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/result_mr_convert_roi_volumes.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-Desikan_dseg.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_T1/anat.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_T1/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_T1/_inputs.pklz @@ -979,11 +839,7 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roiv 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-nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/result_tensor2FA_unmasked.pklz \ No newline at end of file +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/result_tensor2FA_unmasked.pklz diff --git a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt index 4aefd6f6..154d1778 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt @@ -1,31 +1,10 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml 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+cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json @@ -37,47 +16,6 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale2_dseg.nii.gz 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0081a84d..b6cb1e63 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt @@ -1,31 +1,10 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt 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-nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/func_datasinker/result_func_datasinker.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/func_datasource/_inputs.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/func_datasource/_node.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/func_datasource/_report/report.rst @@ -663,16 +526,8 @@ nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_r nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/_node.pklz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/_report/report.rst nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/result_apply_registration_roivs.pklz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale1_dseg_flirt.mat -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale1_dseg_flirt.nii.gz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale2_dseg_flirt.mat -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale2_dseg_flirt.nii.gz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale3_dseg_flirt.mat -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale3_dseg_flirt.nii.gz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale4_dseg_flirt.mat -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale4_dseg_flirt.nii.gz -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale5_dseg_flirt.mat -nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale5_dseg_flirt.nii.gz +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-Desikan_dseg_flirt.mat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-Desikan_dseg_flirt.nii.gz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/eroded_wm_registered.nii.gz From ce591e845956fcc57622ccc4ee3bf6ca8a6194d1 Mon Sep 17 00:00:00 2001 From: Emeline Mullier <43587002+emullier@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:51:11 +0200 Subject: [PATCH 14/26] [fix] Update ds-sample_test-02_outputs.txt --- .../ds-sample_test-02_outputs.txt | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt index 58b68fc2..5e594c0f 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt @@ -1,4 +1,3 @@ -cmp-v3.2.0/dataset_description.json cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv @@ -51,14 +50,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label @@ -95,14 +86,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label From 027c66769466fe749f7471c6b8d023b0311ffe45 Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 12:37:08 +0200 Subject: [PATCH 15/26] [fix] Change expected outputs from ssh circle for test01 test02 and test10 --- .../ds-sample_test-01_outputs.txt | 203 +++------ .../ds-sample_test-02_outputs.txt | 99 ++--- .../ds003505_test-10_outputs.txt | 396 +++++++++--------- 3 files changed, 303 insertions(+), 395 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt index c2679886..53f7951f 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt @@ -1,31 +1,10 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json @@ -38,7 +17,6 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -68,24 +46,9 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label @@ -117,24 +80,9 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label @@ -143,9 +91,10 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz +freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -165,6 +114,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -173,7 +123,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log.bak freesurfer-7.1.1/sub-01_ses-01/mri/norm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/nu.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/orig/001.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig_nu.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz @@ -185,6 +134,7 @@ freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz @@ -196,7 +146,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/segment.dat -freesurfer-7.1.1/sub-01_ses-01/mri/surface.defects.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/talairach.label_intensities.txt @@ -211,14 +160,12 @@ freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm -freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt -freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log @@ -230,10 +177,7 @@ freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.local-copy freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.log freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log -freesurfer-7.1.1/sub-01_ses-01/scripts/recon-config.yaml -freesurfer-7.1.1/sub-01_ses-01/scripts/unknown-args.txt freesurfer-7.1.1/sub-01_ses-01/stats/aseg.stats -freesurfer-7.1.1/sub-01_ses-01/stats/brainvol.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.a2009s.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.pial.stats @@ -251,8 +195,6 @@ freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -262,7 +204,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -270,8 +211,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.BE.crv @@ -302,7 +242,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/rh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.K @@ -310,8 +249,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm.BE.crv @@ -341,6 +279,8 @@ freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.a2009s2aseg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.DKTatlas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/apas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/asegmerge.touch freesurfer-7.1.1/sub-01_ses-01/touch/ca_label.touch @@ -357,26 +297,25 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.pctsurfcon.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.pial_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.qsphere.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphmorph.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphreg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.surfvolume.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.tessellate.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.topofix.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.H.K.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.preaparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.touch 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-nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_report/report.rst -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/result_mgzConvert.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/T1.mgz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/command.txt -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_node.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_report/report.rst -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/result_reconall.pklz diff --git a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt index 5e594c0f..53f7951f 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt @@ -1,3 +1,4 @@ +cmp-v3.2.0/dataset_description.json cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv @@ -16,7 +17,6 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -46,11 +46,9 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label @@ -82,11 +80,9 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label @@ -95,7 +91,7 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz +freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz @@ -127,16 +123,29 @@ freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log.bak freesurfer-7.1.1/sub-01_ses-01/mri/norm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/nu.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/orig/001.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig_nu.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rh.ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/segment.dat -freesurfer-7.1.1/sub-01_ses-01/mri/surface.defects.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/talairach.label_intensities.txt @@ -151,14 +160,12 @@ freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm -freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt -freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log @@ -170,10 +177,7 @@ freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.local-copy freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.log freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log -freesurfer-7.1.1/sub-01_ses-01/scripts/recon-config.yaml -freesurfer-7.1.1/sub-01_ses-01/scripts/unknown-args.txt freesurfer-7.1.1/sub-01_ses-01/stats/aseg.stats -freesurfer-7.1.1/sub-01_ses-01/stats/brainvol.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.a2009s.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.pial.stats @@ -191,8 +195,6 @@ freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -202,7 +204,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -210,8 +211,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.BE.crv @@ -242,7 +242,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/rh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.K @@ -250,8 +249,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm.BE.crv @@ -273,7 +271,16 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.white freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.K +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.Lausanne2018.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.a2009s2aseg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.DKTatlas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/apas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/asegmerge.touch freesurfer-7.1.1/sub-01_ses-01/touch/ca_label.touch @@ -290,26 +297,25 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.pctsurfcon.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.pial_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.qsphere.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphmorph.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphreg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.surfvolume.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.tessellate.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.topofix.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.H.K.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.preaparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.white_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/nu.touch freesurfer-7.1.1/sub-01_ses-01/touch/relabelhypos.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc2.touch @@ -317,31 +323,43 @@ freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.pctsurfcon.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.pial_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.qsphere.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.smoothwm1.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.smoothwm2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.sphmorph.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.sphreg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.surfvolume.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.tessellate.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.topofix.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.white.H.K.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.white.preaparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.white.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.white_surface.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_ca_register.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_em_register.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_em_register.skull.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_fix_topology.lh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_fix_topology.rh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_inflate.lh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_inflate.rh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_register.lh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_register.rh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_sphere.lh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_sphere.rh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_watershed.dat freesurfer-7.1.1/sub-01_ses-01/touch/segstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/skull.lta.touch freesurfer-7.1.1/sub-01_ses-01/touch/skull_strip.touch freesurfer-7.1.1/sub-01_ses-01/touch/talairach.touch freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.stats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.touch freesurfer-7.1.1/sub-01_ses-01/touch/wmsegment.touch nipype-1.8.0/dataset_description.json nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/_inputs.pklz @@ -375,7 +393,9 @@ nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurf nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/csf_mask.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/fsmask_1mm.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/gmmask.nii.gz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_inputs.pklz +age/NativeFreesurfer_parcellation/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_node.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_report/report.rst nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/result_NativeFreesurfer_parcellation.pklz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_inputs.pklz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_node.pklz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_report/report.rst nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/result_NativeFreesurfer_parcellation.pklz @@ -384,18 +404,3 @@ nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurf nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/T1.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/wm_eroded.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_node.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_report/report.rst -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/result_copyOrig.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/command.txt -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_node.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/_report/report.rst -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/result_mgzConvert.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/mgzConvert/T1.mgz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/command.txt -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_node.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/_report/report.rst -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/reconall/result_reconall.pklz diff --git a/.circleci/tests/expected_outputs/ds003505_test-10_outputs.txt b/.circleci/tests/expected_outputs/ds003505_test-10_outputs.txt index 1ba70a0a..7f44361f 100644 --- a/.circleci/tests/expected_outputs/ds003505_test-10_outputs.txt +++ b/.circleci/tests/expected_outputs/ds003505_test-10_outputs.txt @@ -15,51 +15,54 @@ cartool-v3.80/sub-01/eeg/sub-01_eeg.spi cartool-v3.80/sub-01/eeg/sub-01_eeg.xyz cmp-v3.1.0/sub-01/eeg/sub-01_trans.fif cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_stats.tsv -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_stats.tsv -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_stats.tsv -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_stats.tsv cmp-v3.2.0/sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_desc-aseg_dseg.nii.gz -cmp-v3.2.0/sub-01/anat/sub-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_desc-brain_mask.nii.gz +cmp-v3.2.0/sub-01/anat/sub-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_desc-cmp_T1w.json cmp-v3.2.0/sub-01/anat/sub-01_desc-cmp_T1w.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_desc-head_T1w.nii.gz +cmp-v3.2.0/sub-01/anat/sub-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-CSF_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/anat/sub-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/sub-01_anatomical_config.json cmp-v3.2.0/sub-01/sub-01_eeg_config.json eeglab-v14.1.1/dataset_description.json eeglab-v14.1.1/sub-01/eeg/sub-01_task-faces_desc-preproc_eeg.fdt eeglab-v14.1.1/sub-01/eeg/sub-01_task-faces_desc-preproc_eeg.set freesurfer-7.1.1/dataset_description.json -freesurfer-7.1.1/fsaverage/label/Yeo_Brainmap_fsaverage_README +freesurfer-7.1.1/fsaverage/label/lh.aparc.a2005s.annot +freesurfer-7.1.1/fsaverage/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/fsaverage/label/lh.aparc.annot +freesurfer-7.1.1/fsaverage/label/lh.aparc.label freesurfer-7.1.1/fsaverage/label/lh.BA1_exvivo.label freesurfer-7.1.1/fsaverage/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.BA2_exvivo.label @@ -78,18 +81,37 @@ freesurfer-7.1.1/fsaverage/label/lh.BA4p_exvivo.label freesurfer-7.1.1/fsaverage/label/lh.BA4p_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.BA6_exvivo.label freesurfer-7.1.1/fsaverage/label/lh.BA6_exvivo.thresh.label +freesurfer-7.1.1/fsaverage/label/lh.cortex.label +freesurfer-7.1.1/fsaverage/label/lh.entorhinal_exvivo.label +freesurfer-7.1.1/fsaverage/label/lh.entorhinal_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.FG1.mpm.vpnl.label freesurfer-7.1.1/fsaverage/label/lh.FG2.mpm.vpnl.label freesurfer-7.1.1/fsaverage/label/lh.FG3.mpm.vpnl.label freesurfer-7.1.1/fsaverage/label/lh.FG4.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/lh.high-myelin.label +freesurfer-7.1.1/fsaverage/label/lh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/lh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/lh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/lh.hOc4v.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/lh.Medial_wall.label freesurfer-7.1.1/fsaverage/label/lh.MT_exvivo.label freesurfer-7.1.1/fsaverage/label/lh.MT_exvivo.thresh.label -freesurfer-7.1.1/fsaverage/label/lh.Medial_wall.label -freesurfer-7.1.1/fsaverage/label/lh.PALS_B12.labels.gii +freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.annot +freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.ifc.label +freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.ipc.label +freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.ips.label +freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.lateraltemporal.label +freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.medialpfc.label +freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.mtl.label +freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.retrosplenial.label +freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.tp.label freesurfer-7.1.1/fsaverage/label/lh.PALS_B12_Brodmann.annot +freesurfer-7.1.1/fsaverage/label/lh.PALS_B12.labels.gii freesurfer-7.1.1/fsaverage/label/lh.PALS_B12_Lobes.annot freesurfer-7.1.1/fsaverage/label/lh.PALS_B12_OrbitoFrontal.annot freesurfer-7.1.1/fsaverage/label/lh.PALS_B12_Visuotopic.annot +freesurfer-7.1.1/fsaverage/label/lh.perirhinal_exvivo.label +freesurfer-7.1.1/fsaverage/label/lh.perirhinal_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.V1_exvivo.label freesurfer-7.1.1/fsaverage/label/lh.V1_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.V2_exvivo.label @@ -107,29 +129,10 @@ freesurfer-7.1.1/fsaverage/label/lh.Yeo_Brainmap_11Comp_PrActGivenComp.mgz freesurfer-7.1.1/fsaverage/label/lh.Yeo_Brainmap_12Comp_PrActGivenComp.mgz freesurfer-7.1.1/fsaverage/label/lh.Yeo_Brainmap_13Comp_PrActGivenComp.mgz freesurfer-7.1.1/fsaverage/label/lh.Yeo_Brainmap_14Comp_PrActGivenComp.mgz -freesurfer-7.1.1/fsaverage/label/lh.aparc.a2005s.annot -freesurfer-7.1.1/fsaverage/label/lh.aparc.a2009s.annot -freesurfer-7.1.1/fsaverage/label/lh.aparc.annot -freesurfer-7.1.1/fsaverage/label/lh.aparc.label -freesurfer-7.1.1/fsaverage/label/lh.cortex.label -freesurfer-7.1.1/fsaverage/label/lh.entorhinal_exvivo.label -freesurfer-7.1.1/fsaverage/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/fsaverage/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/fsaverage/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/fsaverage/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/fsaverage/label/lh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/fsaverage/label/lh.high-myelin.label -freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.annot -freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.ifc.label -freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.ipc.label -freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.ips.label -freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.lateraltemporal.label -freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.medialpfc.label -freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.mtl.label -freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.retrosplenial.label -freesurfer-7.1.1/fsaverage/label/lh.oasis.chubs.tp.label -freesurfer-7.1.1/fsaverage/label/lh.perirhinal_exvivo.label -freesurfer-7.1.1/fsaverage/label/lh.perirhinal_exvivo.thresh.label +freesurfer-7.1.1/fsaverage/label/rh.aparc.a2005s.annot +freesurfer-7.1.1/fsaverage/label/rh.aparc.a2009s.annot +freesurfer-7.1.1/fsaverage/label/rh.aparc.annot +freesurfer-7.1.1/fsaverage/label/rh.aparc.label freesurfer-7.1.1/fsaverage/label/rh.BA1_exvivo.label freesurfer-7.1.1/fsaverage/label/rh.BA1_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/rh.BA2_exvivo.label @@ -148,18 +151,37 @@ freesurfer-7.1.1/fsaverage/label/rh.BA4p_exvivo.label freesurfer-7.1.1/fsaverage/label/rh.BA4p_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/rh.BA6_exvivo.label freesurfer-7.1.1/fsaverage/label/rh.BA6_exvivo.thresh.label +freesurfer-7.1.1/fsaverage/label/rh.cortex.label +freesurfer-7.1.1/fsaverage/label/rh.entorhinal_exvivo.label +freesurfer-7.1.1/fsaverage/label/rh.entorhinal_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/rh.FG1.mpm.vpnl.label freesurfer-7.1.1/fsaverage/label/rh.FG2.mpm.vpnl.label freesurfer-7.1.1/fsaverage/label/rh.FG3.mpm.vpnl.label freesurfer-7.1.1/fsaverage/label/rh.FG4.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/rh.high-myelin.label +freesurfer-7.1.1/fsaverage/label/rh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/rh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/rh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/rh.hOc4v.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/rh.Medial_wall.label freesurfer-7.1.1/fsaverage/label/rh.MT_exvivo.label freesurfer-7.1.1/fsaverage/label/rh.MT_exvivo.thresh.label -freesurfer-7.1.1/fsaverage/label/rh.Medial_wall.label -freesurfer-7.1.1/fsaverage/label/rh.PALS_B12.labels.gii +freesurfer-7.1.1/fsaverage/label/rh.oasis.chubs.annot +freesurfer-7.1.1/fsaverage/label/rh.oasis.chubs.ifc.label +freesurfer-7.1.1/fsaverage/label/rh.oasis.chubs.ipc.label +freesurfer-7.1.1/fsaverage/label/rh.oasis.chubs.ips.label +freesurfer-7.1.1/fsaverage/label/rh.oasis.chubs.lateraltemporal.label +freesurfer-7.1.1/fsaverage/label/rh.oasis.chubs.medialpfc.label +freesurfer-7.1.1/fsaverage/label/rh.oasis.chubs.mtl.label +freesurfer-7.1.1/fsaverage/label/rh.oasis.chubs.retrosplenial.label +freesurfer-7.1.1/fsaverage/label/rh.oasis.chubs.tp.label freesurfer-7.1.1/fsaverage/label/rh.PALS_B12_Brodmann.annot 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-freesurfer-7.1.1/fsaverage/mri/aparc+aseg.mgz +freesurfer-7.1.1/fsaverage/mri.2mm/T1.mgz freesurfer-7.1.1/fsaverage/mri/aparc.a2005s+aseg.mgz freesurfer-7.1.1/fsaverage/mri/aparc.a2009s+aseg.mgz +freesurfer-7.1.1/fsaverage/mri/aparc+aseg.mgz freesurfer-7.1.1/fsaverage/mri/aseg.mgz -freesurfer-7.1.1/fsaverage/mri/brain.mgz freesurfer-7.1.1/fsaverage/mri/brainmask.mgz +freesurfer-7.1.1/fsaverage/mri/brain.mgz freesurfer-7.1.1/fsaverage/mri/lh.ribbon.mgz freesurfer-7.1.1/fsaverage/mri/mni305.cor.mgz freesurfer-7.1.1/fsaverage/mri/orig.mgz freesurfer-7.1.1/fsaverage/mri/p.aseg.mgz freesurfer-7.1.1/fsaverage/mri/rh.ribbon.mgz freesurfer-7.1.1/fsaverage/mri/ribbon.mgz -freesurfer-7.1.1/fsaverage/mri/subcort.mask.1mm.README freesurfer-7.1.1/fsaverage/mri/subcort.mask.1mm.mgz +freesurfer-7.1.1/fsaverage/mri/subcort.mask.1mm.README freesurfer-7.1.1/fsaverage/mri/subcort.prob.log freesurfer-7.1.1/fsaverage/mri/subcort.prob.mgz +freesurfer-7.1.1/fsaverage/mri/T1.mgz freesurfer-7.1.1/fsaverage/mri/transforms/reg.mni152.2mm.dat freesurfer-7.1.1/fsaverage/mri/transforms/talairach.xfm freesurfer-7.1.1/fsaverage/scripts/build-stamp.txt @@ -235,16 +235,16 @@ freesurfer-7.1.1/fsaverage/scripts/cvs_log_pre_31May2011.txt freesurfer-7.1.1/fsaverage/scripts/fix-surf7.log freesurfer-7.1.1/fsaverage/scripts/make_average_surface.log freesurfer-7.1.1/fsaverage/scripts/make_average_volume.log -freesurfer-7.1.1/fsaverage/scripts/mris_inflate.log freesurfer-7.1.1/fsaverage/scripts/mris_inflate_lh.log +freesurfer-7.1.1/fsaverage/scripts/mris_inflate.log freesurfer-7.1.1/fsaverage/scripts/mris_inflate_rh.log -freesurfer-7.1.1/fsaverage/scripts/recon-all-status.log freesurfer-7.1.1/fsaverage/scripts/recon-all.cmd freesurfer-7.1.1/fsaverage/scripts/recon-all.done freesurfer-7.1.1/fsaverage/scripts/recon-all.env freesurfer-7.1.1/fsaverage/scripts/recon-all.env.bak freesurfer-7.1.1/fsaverage/scripts/recon-all.local-copy freesurfer-7.1.1/fsaverage/scripts/recon-all.log +freesurfer-7.1.1/fsaverage/scripts/recon-all-status.log freesurfer-7.1.1/fsaverage/scripts/surfreg.fsaverage_sym.lh.log freesurfer-7.1.1/fsaverage/scripts/surfreg.fsaverage_sym.rh.log freesurfer-7.1.1/fsaverage/surf/lh.area @@ -256,16 +256,16 @@ freesurfer-7.1.1/fsaverage/surf/lh.cortex.patch.flat freesurfer-7.1.1/fsaverage/surf/lh.curv freesurfer-7.1.1/fsaverage/surf/lh.fsaverage_sym.sphere.reg freesurfer-7.1.1/fsaverage/surf/lh.inflated +freesurfer-7.1.1/fsaverage/surf/lh.inflated_avg freesurfer-7.1.1/fsaverage/surf/lh.inflated.H freesurfer-7.1.1/fsaverage/surf/lh.inflated.K -freesurfer-7.1.1/fsaverage/surf/lh.inflated_avg freesurfer-7.1.1/fsaverage/surf/lh.inflated_pre freesurfer-7.1.1/fsaverage/surf/lh.orig -freesurfer-7.1.1/fsaverage/surf/lh.orig.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.orig_avg +freesurfer-7.1.1/fsaverage/surf/lh.orig.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.pial -freesurfer-7.1.1/fsaverage/surf/lh.pial.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.pial_avg +freesurfer-7.1.1/fsaverage/surf/lh.pial.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.pial_semi_inflated freesurfer-7.1.1/fsaverage/surf/lh.smoothwm freesurfer-7.1.1/fsaverage/surf/lh.sphere @@ -274,8 +274,8 @@ freesurfer-7.1.1/fsaverage/surf/lh.sphere.reg.avg freesurfer-7.1.1/fsaverage/surf/lh.sulc freesurfer-7.1.1/fsaverage/surf/lh.thickness freesurfer-7.1.1/fsaverage/surf/lh.white -freesurfer-7.1.1/fsaverage/surf/lh.white.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.white_avg +freesurfer-7.1.1/fsaverage/surf/lh.white.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.white_avg.H freesurfer-7.1.1/fsaverage/surf/lh.white_avg.K freesurfer-7.1.1/fsaverage/surf/mris_preproc.surface.lh.log @@ -289,16 +289,16 @@ freesurfer-7.1.1/fsaverage/surf/rh.cortex.patch.flat freesurfer-7.1.1/fsaverage/surf/rh.curv freesurfer-7.1.1/fsaverage/surf/rh.fsaverage_sym.sphere.reg freesurfer-7.1.1/fsaverage/surf/rh.inflated +freesurfer-7.1.1/fsaverage/surf/rh.inflated_avg freesurfer-7.1.1/fsaverage/surf/rh.inflated.H freesurfer-7.1.1/fsaverage/surf/rh.inflated.K -freesurfer-7.1.1/fsaverage/surf/rh.inflated_avg freesurfer-7.1.1/fsaverage/surf/rh.inflated_pre freesurfer-7.1.1/fsaverage/surf/rh.orig -freesurfer-7.1.1/fsaverage/surf/rh.orig.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.orig_avg +freesurfer-7.1.1/fsaverage/surf/rh.orig.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.pial -freesurfer-7.1.1/fsaverage/surf/rh.pial.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.pial_avg +freesurfer-7.1.1/fsaverage/surf/rh.pial.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.pial_semi_inflated freesurfer-7.1.1/fsaverage/surf/rh.smoothwm freesurfer-7.1.1/fsaverage/surf/rh.sphere @@ -307,8 +307,8 @@ freesurfer-7.1.1/fsaverage/surf/rh.sphere.reg.avg freesurfer-7.1.1/fsaverage/surf/rh.sulc freesurfer-7.1.1/fsaverage/surf/rh.thickness freesurfer-7.1.1/fsaverage/surf/rh.white -freesurfer-7.1.1/fsaverage/surf/rh.white.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.white_avg +freesurfer-7.1.1/fsaverage/surf/rh.white.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.white_avg.H freesurfer-7.1.1/fsaverage/surf/rh.white_avg.K freesurfer-7.1.1/fsaverage/xhemi/label/lh.aparc.a2009s.annot @@ -319,27 +319,27 @@ freesurfer-7.1.1/fsaverage/xhemi/label/rh.aparc.annot freesurfer-7.1.1/fsaverage/xhemi/label/rh.cortex.label freesurfer-7.1.1/fsaverage/xhemi/lrrev.pure.register.dat freesurfer-7.1.1/fsaverage/xhemi/lrrev.register.dat -freesurfer-7.1.1/fsaverage/xhemi/mri/T1.mgz freesurfer-7.1.1/fsaverage/xhemi/mri/aparc+aseg.mgz freesurfer-7.1.1/fsaverage/xhemi/mri/aseg.mgz -freesurfer-7.1.1/fsaverage/xhemi/mri/brain.mgz freesurfer-7.1.1/fsaverage/xhemi/mri/brainmask.mgz +freesurfer-7.1.1/fsaverage/xhemi/mri/brain.mgz freesurfer-7.1.1/fsaverage/xhemi/mri/mri_nu_correct.mni.log freesurfer-7.1.1/fsaverage/xhemi/mri/orig.mgz freesurfer-7.1.1/fsaverage/xhemi/mri/orig_nu.mgz +freesurfer-7.1.1/fsaverage/xhemi/mri/T1.mgz freesurfer-7.1.1/fsaverage/xhemi/mri/transforms/talairach.auto.xfm -freesurfer-7.1.1/fsaverage/xhemi/mri/transforms/talairach.xfm freesurfer-7.1.1/fsaverage/xhemi/mri/transforms/talairach_avi.log +freesurfer-7.1.1/fsaverage/xhemi/mri/transforms/talairach.xfm freesurfer-7.1.1/fsaverage/xhemi/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/fsaverage/xhemi/scripts/build-stamp.txt freesurfer-7.1.1/fsaverage/xhemi/scripts/lastcall.build-stamp.txt freesurfer-7.1.1/fsaverage/xhemi/scripts/patchdir.txt -freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all-status.log freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.cmd freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.done freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.env freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.local-copy freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.log +freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all-status.log freesurfer-7.1.1/fsaverage/xhemi/scripts/surfreg.fsaverage_sym.lh.log freesurfer-7.1.1/fsaverage/xhemi/scripts/surfreg.fsaverage_sym.rh.log freesurfer-7.1.1/fsaverage/xhemi/surf/lh.area @@ -381,11 +381,14 @@ freesurfer-7.1.1/sub-01/bem/watershed/sub-01_inner_skull_surface freesurfer-7.1.1/sub-01/bem/watershed/sub-01_outer_skin_surface freesurfer-7.1.1/sub-01/bem/watershed/sub-01_outer_skull_surface freesurfer-7.1.1/sub-01/bem/watershed/ws.mgz -freesurfer-7.1.1/sub-01/label/BA_exvivo.ctab -freesurfer-7.1.1/sub-01/label/BA_exvivo.thresh.ctab -freesurfer-7.1.1/sub-01/label/aparc.annot.DKTatlas.ctab freesurfer-7.1.1/sub-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01/label/aparc.annot.ctab +freesurfer-7.1.1/sub-01/label/aparc.annot.DKTatlas.ctab +freesurfer-7.1.1/sub-01/label/BA_exvivo.ctab +freesurfer-7.1.1/sub-01/label/BA_exvivo.thresh.ctab +freesurfer-7.1.1/sub-01/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01/label/lh.BA2_exvivo.label @@ -406,23 +409,14 @@ freesurfer-7.1.1/sub-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01/label/lh.MT_exvivo.label -freesurfer-7.1.1/sub-01/label/lh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01/label/lh.V1_exvivo.label -freesurfer-7.1.1/sub-01/label/lh.V1_exvivo.thresh.label -freesurfer-7.1.1/sub-01/label/lh.V2_exvivo.label -freesurfer-7.1.1/sub-01/label/lh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01/label/lh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01/label/lh.aparc.a2009s.annot -freesurfer-7.1.1/sub-01/label/lh.aparc.annot freesurfer-7.1.1/sub-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01/label/lh.cortex.label freesurfer-7.1.1/sub-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01/label/lh.entorhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01/label/lh.FG1.mpm.vpnl.label +freesurfer-7.1.1/sub-01/label/lh.FG2.mpm.vpnl.label +freesurfer-7.1.1/sub-01/label/lh.FG3.mpm.vpnl.label +freesurfer-7.1.1/sub-01/label/lh.FG4.mpm.vpnl.label freesurfer-7.1.1/sub-01/label/lh.hOc1.mpm.vpnl.label freesurfer-7.1.1/sub-01/label/lh.hOc2.mpm.vpnl.label freesurfer-7.1.1/sub-01/label/lh.hOc3v.mpm.vpnl.label @@ -433,8 +427,17 @@ freesurfer-7.1.1/sub-01/label/lh.lausanne2018.scale3.annot freesurfer-7.1.1/sub-01/label/lh.lausanne2018.scale4.annot freesurfer-7.1.1/sub-01/label/lh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01/label/lh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01/label/lh.MT_exvivo.label +freesurfer-7.1.1/sub-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01/label/lh.perirhinal_exvivo.label freesurfer-7.1.1/sub-01/label/lh.perirhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01/label/lh.V1_exvivo.label +freesurfer-7.1.1/sub-01/label/lh.V1_exvivo.thresh.label +freesurfer-7.1.1/sub-01/label/lh.V2_exvivo.label +freesurfer-7.1.1/sub-01/label/lh.V2_exvivo.thresh.label +freesurfer-7.1.1/sub-01/label/rh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01/label/rh.aparc.annot +freesurfer-7.1.1/sub-01/label/rh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01/label/rh.BA1_exvivo.label freesurfer-7.1.1/sub-01/label/rh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01/label/rh.BA2_exvivo.label @@ -455,23 +458,14 @@ freesurfer-7.1.1/sub-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01/label/rh.BA_exvivo.thresh.annot 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-freesurfer-7.1.1/sub-01/mri/transforms/talairach_with_skull.lta freesurfer-7.1.1/sub-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/sub-01/mri/wm.asegedit.mgz freesurfer-7.1.1/sub-01/mri/wm.mgz -freesurfer-7.1.1/sub-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01/mri/wmparc.mgz +freesurfer-7.1.1/sub-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01/scripts/build-stamp.txt freesurfer-7.1.1/sub-01/scripts/defect2seg.log freesurfer-7.1.1/sub-01/scripts/lastcall.build-stamp.txt @@ -565,30 +565,30 @@ freesurfer-7.1.1/sub-01/scripts/patchdir.txt freesurfer-7.1.1/sub-01/scripts/pctsurfcon.log freesurfer-7.1.1/sub-01/scripts/pctsurfcon.log.old freesurfer-7.1.1/sub-01/scripts/ponscc.cut.log -freesurfer-7.1.1/sub-01/scripts/recon-all-status.log freesurfer-7.1.1/sub-01/scripts/recon-all.cmd freesurfer-7.1.1/sub-01/scripts/recon-all.done freesurfer-7.1.1/sub-01/scripts/recon-all.env freesurfer-7.1.1/sub-01/scripts/recon-all.local-copy freesurfer-7.1.1/sub-01/scripts/recon-all.log +freesurfer-7.1.1/sub-01/scripts/recon-all-status.log freesurfer-7.1.1/sub-01/scripts/recon-config.yaml freesurfer-7.1.1/sub-01/scripts/unknown-args.txt freesurfer-7.1.1/sub-01/stats/aseg.stats freesurfer-7.1.1/sub-01/stats/brainvol.stats -freesurfer-7.1.1/sub-01/stats/lh.BA_exvivo.stats -freesurfer-7.1.1/sub-01/stats/lh.BA_exvivo.thresh.stats -freesurfer-7.1.1/sub-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01/stats/lh.aparc.a2009s.stats +freesurfer-7.1.1/sub-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01/stats/lh.aparc.pial.stats freesurfer-7.1.1/sub-01/stats/lh.aparc.stats +freesurfer-7.1.1/sub-01/stats/lh.BA_exvivo.stats +freesurfer-7.1.1/sub-01/stats/lh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01/stats/lh.curv.stats freesurfer-7.1.1/sub-01/stats/lh.w-g.pct.stats -freesurfer-7.1.1/sub-01/stats/rh.BA_exvivo.stats -freesurfer-7.1.1/sub-01/stats/rh.BA_exvivo.thresh.stats -freesurfer-7.1.1/sub-01/stats/rh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01/stats/rh.aparc.a2009s.stats +freesurfer-7.1.1/sub-01/stats/rh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01/stats/rh.aparc.pial.stats freesurfer-7.1.1/sub-01/stats/rh.aparc.stats +freesurfer-7.1.1/sub-01/stats/rh.BA_exvivo.stats +freesurfer-7.1.1/sub-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01/stats/wmparc.stats @@ -620,11 +620,11 @@ freesurfer-7.1.1/sub-01/surf/lh.smoothwm.BE.crv freesurfer-7.1.1/sub-01/surf/lh.smoothwm.C.crv freesurfer-7.1.1/sub-01/surf/lh.smoothwm.FI.crv freesurfer-7.1.1/sub-01/surf/lh.smoothwm.H.crv -freesurfer-7.1.1/sub-01/surf/lh.smoothwm.K.crv freesurfer-7.1.1/sub-01/surf/lh.smoothwm.K1.crv freesurfer-7.1.1/sub-01/surf/lh.smoothwm.K2.crv -freesurfer-7.1.1/sub-01/surf/lh.smoothwm.S.crv +freesurfer-7.1.1/sub-01/surf/lh.smoothwm.K.crv freesurfer-7.1.1/sub-01/surf/lh.smoothwm.nofix +freesurfer-7.1.1/sub-01/surf/lh.smoothwm.S.crv freesurfer-7.1.1/sub-01/surf/lh.sphere freesurfer-7.1.1/sub-01/surf/lh.sphere.reg freesurfer-7.1.1/sub-01/surf/lh.sulc @@ -663,11 +663,11 @@ freesurfer-7.1.1/sub-01/surf/rh.smoothwm.BE.crv freesurfer-7.1.1/sub-01/surf/rh.smoothwm.C.crv freesurfer-7.1.1/sub-01/surf/rh.smoothwm.FI.crv freesurfer-7.1.1/sub-01/surf/rh.smoothwm.H.crv -freesurfer-7.1.1/sub-01/surf/rh.smoothwm.K.crv freesurfer-7.1.1/sub-01/surf/rh.smoothwm.K1.crv freesurfer-7.1.1/sub-01/surf/rh.smoothwm.K2.crv -freesurfer-7.1.1/sub-01/surf/rh.smoothwm.S.crv +freesurfer-7.1.1/sub-01/surf/rh.smoothwm.K.crv freesurfer-7.1.1/sub-01/surf/rh.smoothwm.nofix +freesurfer-7.1.1/sub-01/surf/rh.smoothwm.S.crv freesurfer-7.1.1/sub-01/surf/rh.sphere freesurfer-7.1.1/sub-01/surf/rh.sphere.reg freesurfer-7.1.1/sub-01/surf/rh.sulc @@ -680,14 +680,14 @@ freesurfer-7.1.1/sub-01/surf/rh.white.K freesurfer-7.1.1/sub-01/surf/rh.white.preaparc freesurfer-7.1.1/sub-01/surf/rh.white.preaparc.H 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-nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/result_parcCombiner.pklz -nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3.nii.gz +nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ROIv_Lausanne2018_scale5_FreeSurferColorLUT.txt +nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ROIv_Lausanne2018_scale5.graphml nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3_dil.nii.gz +nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3.nii.gz nipype-1.8.0/sub-01/anatomical_pipeline/pypeline.log nipype-1.8.0/sub-01/eeg_pipeline/eeg_check_input/_inputs.pklz nipype-1.8.0/sub-01/eeg_pipeline/eeg_check_input/_node.pklz From b95c5498d09e6c3f2dbf611217829e3ef67c16a1 Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 15:03:27 +0200 Subject: [PATCH 16/26] [fix] New update test01, test02 and test10 --- .../ds-sample_test-01_outputs.txt | 115 +- .../ds-sample_test-02_outputs.txt | 5 +- .../ds003505_test-10_outputs.txt | 1239 ++++++----------- 3 files changed, 494 insertions(+), 865 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt index 53f7951f..566809a3 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt @@ -1,10 +1,31 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv 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+nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/result_NativeFreesurfer_parcellation.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_inputs.pklz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_node.pklz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_report/report.rst nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/result_NativeFreesurfer_parcellation.pklz diff --git a/.circleci/tests/expected_outputs/ds003505_test-10_outputs.txt b/.circleci/tests/expected_outputs/ds003505_test-10_outputs.txt index 7f44361f..53f7951f 100644 --- a/.circleci/tests/expected_outputs/ds003505_test-10_outputs.txt +++ b/.circleci/tests/expected_outputs/ds003505_test-10_outputs.txt @@ -1,839 +1,406 @@ -cartool-v3.80/dataset_description.json -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale1.pickle.rois -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale1.rois -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale2.pickle.rois -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale2.rois -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale3.pickle.rois -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale3.rois -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale4.pickle.rois -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale4.rois -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale5.pickle.rois -cartool-v3.80/sub-01/eeg/rois/sub-01_label-L2008_desc-scale5.rois -cartool-v3.80/sub-01/eeg/sub-01_eeg.LAURA.is -cartool-v3.80/sub-01/eeg/sub-01_eeg.LORETA.is -cartool-v3.80/sub-01/eeg/sub-01_eeg.spi -cartool-v3.80/sub-01/eeg/sub-01_eeg.xyz -cmp-v3.1.0/sub-01/eeg/sub-01_trans.fif cmp-v3.2.0/dataset_description.json 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+nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_report/report.rst +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/result_NativeFreesurfer_parcellation.pklz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/ribbon.nii.gz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/ROIv_HR_th_freesurferaparc.nii.gz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/T1.nii.gz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/wm_eroded.nii.gz +nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log From 4ad61d20c8b867074c301c74c049e7fc8921d872 Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 15:31:36 +0200 Subject: [PATCH 17/26] [upd] Update in config.yml all the singularity version to 3.8.4 --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 48b299fc..91cf0f7c 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1489,7 +1489,7 @@ jobs: - singularity/install-go: go-version: '1.13.15' - singularity/debian-install-3: - singularity-version: 3.6.3 + singularity-version: 3.8.4 - install-conda-and-cmp3: run_name: "Setup miniconda environment and install connectomemapper3 with Python wrappers" cmp3_dir: /home/circleci/src/connectomemapper3 From b582a9b431309914451c32664e0e9fac89935bdf Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 15:53:12 +0200 Subject: [PATCH 18/26] [upd] Update test11 --- .../ds003505_test-11_outputs.txt | 398 +++++++++--------- 1 file changed, 199 insertions(+), 199 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds003505_test-11_outputs.txt b/.circleci/tests/expected_outputs/ds003505_test-11_outputs.txt index db7a83a3..2b1ea5c3 100644 --- a/.circleci/tests/expected_outputs/ds003505_test-11_outputs.txt +++ b/.circleci/tests/expected_outputs/ds003505_test-11_outputs.txt @@ -15,51 +15,54 @@ cartool-v3.80/sub-01/eeg/sub-01_eeg.spi cartool-v3.80/sub-01/eeg/sub-01_eeg.xyz cmp-v3.1.0/sub-01/eeg/sub-01_trans.fif cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale2_stats.tsv -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale3_stats.tsv -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale4_stats.tsv -cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_dseg.graphml cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/anat/sub-01_atlas-L2018_res-scale5_stats.tsv cmp-v3.2.0/sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_desc-aseg_dseg.nii.gz -cmp-v3.2.0/sub-01/anat/sub-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_desc-brain_mask.nii.gz +cmp-v3.2.0/sub-01/anat/sub-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_desc-cmp_T1w.json cmp-v3.2.0/sub-01/anat/sub-01_desc-cmp_T1w.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_desc-head_T1w.nii.gz +cmp-v3.2.0/sub-01/anat/sub-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-CSF_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/anat/sub-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/anat/sub-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/sub-01_anatomical_config.json cmp-v3.2.0/sub-01/sub-01_eeg_config.json eeglab-v14.1.1/dataset_description.json eeglab-v14.1.1/sub-01/eeg/sub-01_task-faces_desc-preproc_eeg.fdt eeglab-v14.1.1/sub-01/eeg/sub-01_task-faces_desc-preproc_eeg.set freesurfer-7.1.1/dataset_description.json -freesurfer-7.1.1/fsaverage/label/Yeo_Brainmap_fsaverage_README +freesurfer-7.1.1/fsaverage/label/lh.aparc.a2005s.annot +freesurfer-7.1.1/fsaverage/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/fsaverage/label/lh.aparc.annot +freesurfer-7.1.1/fsaverage/label/lh.aparc.label freesurfer-7.1.1/fsaverage/label/lh.BA1_exvivo.label freesurfer-7.1.1/fsaverage/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.BA2_exvivo.label @@ -78,18 +81,37 @@ freesurfer-7.1.1/fsaverage/label/lh.BA4p_exvivo.label freesurfer-7.1.1/fsaverage/label/lh.BA4p_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.BA6_exvivo.label freesurfer-7.1.1/fsaverage/label/lh.BA6_exvivo.thresh.label +freesurfer-7.1.1/fsaverage/label/lh.cortex.label +freesurfer-7.1.1/fsaverage/label/lh.entorhinal_exvivo.label +freesurfer-7.1.1/fsaverage/label/lh.entorhinal_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.FG1.mpm.vpnl.label freesurfer-7.1.1/fsaverage/label/lh.FG2.mpm.vpnl.label freesurfer-7.1.1/fsaverage/label/lh.FG3.mpm.vpnl.label freesurfer-7.1.1/fsaverage/label/lh.FG4.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/lh.high-myelin.label +freesurfer-7.1.1/fsaverage/label/lh.hOc1.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/lh.hOc2.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/lh.hOc3v.mpm.vpnl.label +freesurfer-7.1.1/fsaverage/label/lh.hOc4v.mpm.vpnl.label 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freesurfer-7.1.1/fsaverage/label/lh.PALS_B12_Lobes.annot freesurfer-7.1.1/fsaverage/label/lh.PALS_B12_OrbitoFrontal.annot freesurfer-7.1.1/fsaverage/label/lh.PALS_B12_Visuotopic.annot +freesurfer-7.1.1/fsaverage/label/lh.perirhinal_exvivo.label +freesurfer-7.1.1/fsaverage/label/lh.perirhinal_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.V1_exvivo.label freesurfer-7.1.1/fsaverage/label/lh.V1_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/lh.V2_exvivo.label @@ -107,29 +129,10 @@ freesurfer-7.1.1/fsaverage/label/lh.Yeo_Brainmap_11Comp_PrActGivenComp.mgz freesurfer-7.1.1/fsaverage/label/lh.Yeo_Brainmap_12Comp_PrActGivenComp.mgz freesurfer-7.1.1/fsaverage/label/lh.Yeo_Brainmap_13Comp_PrActGivenComp.mgz freesurfer-7.1.1/fsaverage/label/lh.Yeo_Brainmap_14Comp_PrActGivenComp.mgz -freesurfer-7.1.1/fsaverage/label/lh.aparc.a2005s.annot -freesurfer-7.1.1/fsaverage/label/lh.aparc.a2009s.annot -freesurfer-7.1.1/fsaverage/label/lh.aparc.annot 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freesurfer-7.1.1/fsaverage/label/rh.V2_exvivo.label @@ -177,57 +199,35 @@ freesurfer-7.1.1/fsaverage/label/rh.Yeo_Brainmap_11Comp_PrActGivenComp.mgz freesurfer-7.1.1/fsaverage/label/rh.Yeo_Brainmap_12Comp_PrActGivenComp.mgz freesurfer-7.1.1/fsaverage/label/rh.Yeo_Brainmap_13Comp_PrActGivenComp.mgz freesurfer-7.1.1/fsaverage/label/rh.Yeo_Brainmap_14Comp_PrActGivenComp.mgz -freesurfer-7.1.1/fsaverage/label/rh.aparc.a2005s.annot -freesurfer-7.1.1/fsaverage/label/rh.aparc.a2009s.annot -freesurfer-7.1.1/fsaverage/label/rh.aparc.annot -freesurfer-7.1.1/fsaverage/label/rh.aparc.label -freesurfer-7.1.1/fsaverage/label/rh.cortex.label -freesurfer-7.1.1/fsaverage/label/rh.entorhinal_exvivo.label -freesurfer-7.1.1/fsaverage/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/fsaverage/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/fsaverage/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/fsaverage/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/fsaverage/label/rh.hOc4v.mpm.vpnl.label 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freesurfer-7.1.1/fsaverage/mri.2mm/brainmask.mgz +freesurfer-7.1.1/fsaverage/mri.2mm/brain.mgz freesurfer-7.1.1/fsaverage/mri.2mm/mni305.cor.mgz freesurfer-7.1.1/fsaverage/mri.2mm/orig.mgz +freesurfer-7.1.1/fsaverage/mri.2mm/README freesurfer-7.1.1/fsaverage/mri.2mm/reg.2mm.dat freesurfer-7.1.1/fsaverage/mri.2mm/reg.2mm.mni152.dat freesurfer-7.1.1/fsaverage/mri.2mm/subcort.mask.mgz freesurfer-7.1.1/fsaverage/mri.2mm/subcort.prob.mgz -freesurfer-7.1.1/fsaverage/mri/T1.mgz -freesurfer-7.1.1/fsaverage/mri/aparc+aseg.mgz +freesurfer-7.1.1/fsaverage/mri.2mm/T1.mgz freesurfer-7.1.1/fsaverage/mri/aparc.a2005s+aseg.mgz freesurfer-7.1.1/fsaverage/mri/aparc.a2009s+aseg.mgz +freesurfer-7.1.1/fsaverage/mri/aparc+aseg.mgz freesurfer-7.1.1/fsaverage/mri/aseg.mgz -freesurfer-7.1.1/fsaverage/mri/brain.mgz freesurfer-7.1.1/fsaverage/mri/brainmask.mgz +freesurfer-7.1.1/fsaverage/mri/brain.mgz freesurfer-7.1.1/fsaverage/mri/lh.ribbon.mgz freesurfer-7.1.1/fsaverage/mri/mni305.cor.mgz freesurfer-7.1.1/fsaverage/mri/orig.mgz freesurfer-7.1.1/fsaverage/mri/p.aseg.mgz freesurfer-7.1.1/fsaverage/mri/rh.ribbon.mgz freesurfer-7.1.1/fsaverage/mri/ribbon.mgz -freesurfer-7.1.1/fsaverage/mri/subcort.mask.1mm.README freesurfer-7.1.1/fsaverage/mri/subcort.mask.1mm.mgz +freesurfer-7.1.1/fsaverage/mri/subcort.mask.1mm.README freesurfer-7.1.1/fsaverage/mri/subcort.prob.log freesurfer-7.1.1/fsaverage/mri/subcort.prob.mgz +freesurfer-7.1.1/fsaverage/mri/T1.mgz freesurfer-7.1.1/fsaverage/mri/transforms/reg.mni152.2mm.dat freesurfer-7.1.1/fsaverage/mri/transforms/talairach.xfm freesurfer-7.1.1/fsaverage/scripts/build-stamp.txt @@ -235,16 +235,16 @@ freesurfer-7.1.1/fsaverage/scripts/cvs_log_pre_31May2011.txt freesurfer-7.1.1/fsaverage/scripts/fix-surf7.log freesurfer-7.1.1/fsaverage/scripts/make_average_surface.log freesurfer-7.1.1/fsaverage/scripts/make_average_volume.log -freesurfer-7.1.1/fsaverage/scripts/mris_inflate.log freesurfer-7.1.1/fsaverage/scripts/mris_inflate_lh.log +freesurfer-7.1.1/fsaverage/scripts/mris_inflate.log freesurfer-7.1.1/fsaverage/scripts/mris_inflate_rh.log -freesurfer-7.1.1/fsaverage/scripts/recon-all-status.log freesurfer-7.1.1/fsaverage/scripts/recon-all.cmd freesurfer-7.1.1/fsaverage/scripts/recon-all.done freesurfer-7.1.1/fsaverage/scripts/recon-all.env freesurfer-7.1.1/fsaverage/scripts/recon-all.env.bak freesurfer-7.1.1/fsaverage/scripts/recon-all.local-copy freesurfer-7.1.1/fsaverage/scripts/recon-all.log +freesurfer-7.1.1/fsaverage/scripts/recon-all-status.log freesurfer-7.1.1/fsaverage/scripts/surfreg.fsaverage_sym.lh.log freesurfer-7.1.1/fsaverage/scripts/surfreg.fsaverage_sym.rh.log freesurfer-7.1.1/fsaverage/surf/lh.area @@ -256,16 +256,16 @@ freesurfer-7.1.1/fsaverage/surf/lh.cortex.patch.flat freesurfer-7.1.1/fsaverage/surf/lh.curv freesurfer-7.1.1/fsaverage/surf/lh.fsaverage_sym.sphere.reg freesurfer-7.1.1/fsaverage/surf/lh.inflated +freesurfer-7.1.1/fsaverage/surf/lh.inflated_avg freesurfer-7.1.1/fsaverage/surf/lh.inflated.H freesurfer-7.1.1/fsaverage/surf/lh.inflated.K -freesurfer-7.1.1/fsaverage/surf/lh.inflated_avg freesurfer-7.1.1/fsaverage/surf/lh.inflated_pre freesurfer-7.1.1/fsaverage/surf/lh.orig -freesurfer-7.1.1/fsaverage/surf/lh.orig.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.orig_avg +freesurfer-7.1.1/fsaverage/surf/lh.orig.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.pial -freesurfer-7.1.1/fsaverage/surf/lh.pial.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.pial_avg +freesurfer-7.1.1/fsaverage/surf/lh.pial.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.pial_semi_inflated freesurfer-7.1.1/fsaverage/surf/lh.smoothwm freesurfer-7.1.1/fsaverage/surf/lh.sphere @@ -274,8 +274,8 @@ freesurfer-7.1.1/fsaverage/surf/lh.sphere.reg.avg freesurfer-7.1.1/fsaverage/surf/lh.sulc freesurfer-7.1.1/fsaverage/surf/lh.thickness freesurfer-7.1.1/fsaverage/surf/lh.white -freesurfer-7.1.1/fsaverage/surf/lh.white.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.white_avg +freesurfer-7.1.1/fsaverage/surf/lh.white.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/lh.white_avg.H freesurfer-7.1.1/fsaverage/surf/lh.white_avg.K freesurfer-7.1.1/fsaverage/surf/mris_preproc.surface.lh.log @@ -289,16 +289,16 @@ freesurfer-7.1.1/fsaverage/surf/rh.cortex.patch.flat freesurfer-7.1.1/fsaverage/surf/rh.curv freesurfer-7.1.1/fsaverage/surf/rh.fsaverage_sym.sphere.reg freesurfer-7.1.1/fsaverage/surf/rh.inflated +freesurfer-7.1.1/fsaverage/surf/rh.inflated_avg freesurfer-7.1.1/fsaverage/surf/rh.inflated.H freesurfer-7.1.1/fsaverage/surf/rh.inflated.K -freesurfer-7.1.1/fsaverage/surf/rh.inflated_avg freesurfer-7.1.1/fsaverage/surf/rh.inflated_pre freesurfer-7.1.1/fsaverage/surf/rh.orig -freesurfer-7.1.1/fsaverage/surf/rh.orig.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.orig_avg +freesurfer-7.1.1/fsaverage/surf/rh.orig.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.pial -freesurfer-7.1.1/fsaverage/surf/rh.pial.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.pial_avg +freesurfer-7.1.1/fsaverage/surf/rh.pial.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.pial_semi_inflated freesurfer-7.1.1/fsaverage/surf/rh.smoothwm freesurfer-7.1.1/fsaverage/surf/rh.sphere @@ -307,8 +307,8 @@ freesurfer-7.1.1/fsaverage/surf/rh.sphere.reg.avg freesurfer-7.1.1/fsaverage/surf/rh.sulc freesurfer-7.1.1/fsaverage/surf/rh.thickness freesurfer-7.1.1/fsaverage/surf/rh.white -freesurfer-7.1.1/fsaverage/surf/rh.white.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.white_avg +freesurfer-7.1.1/fsaverage/surf/rh.white.avg.area.mgh freesurfer-7.1.1/fsaverage/surf/rh.white_avg.H freesurfer-7.1.1/fsaverage/surf/rh.white_avg.K freesurfer-7.1.1/fsaverage/xhemi/label/lh.aparc.a2009s.annot @@ -319,27 +319,27 @@ freesurfer-7.1.1/fsaverage/xhemi/label/rh.aparc.annot freesurfer-7.1.1/fsaverage/xhemi/label/rh.cortex.label freesurfer-7.1.1/fsaverage/xhemi/lrrev.pure.register.dat freesurfer-7.1.1/fsaverage/xhemi/lrrev.register.dat 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freesurfer-7.1.1/fsaverage/xhemi/scripts/patchdir.txt -freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all-status.log freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.cmd freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.done freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.env freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.local-copy freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all.log +freesurfer-7.1.1/fsaverage/xhemi/scripts/recon-all-status.log freesurfer-7.1.1/fsaverage/xhemi/scripts/surfreg.fsaverage_sym.lh.log freesurfer-7.1.1/fsaverage/xhemi/scripts/surfreg.fsaverage_sym.rh.log freesurfer-7.1.1/fsaverage/xhemi/surf/lh.area @@ -381,11 +381,14 @@ freesurfer-7.1.1/sub-01/bem/watershed/sub-01_inner_skull_surface freesurfer-7.1.1/sub-01/bem/watershed/sub-01_outer_skin_surface freesurfer-7.1.1/sub-01/bem/watershed/sub-01_outer_skull_surface freesurfer-7.1.1/sub-01/bem/watershed/ws.mgz -freesurfer-7.1.1/sub-01/label/BA_exvivo.ctab -freesurfer-7.1.1/sub-01/label/BA_exvivo.thresh.ctab -freesurfer-7.1.1/sub-01/label/aparc.annot.DKTatlas.ctab freesurfer-7.1.1/sub-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01/label/aparc.annot.ctab +freesurfer-7.1.1/sub-01/label/aparc.annot.DKTatlas.ctab +freesurfer-7.1.1/sub-01/label/BA_exvivo.ctab +freesurfer-7.1.1/sub-01/label/BA_exvivo.thresh.ctab +freesurfer-7.1.1/sub-01/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01/label/lh.BA2_exvivo.label @@ -406,23 +409,14 @@ freesurfer-7.1.1/sub-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01/label/lh.FG1.mpm.vpnl.label 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+freesurfer-7.1.1/sub-01/label/rh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01/label/rh.aparc.annot +freesurfer-7.1.1/sub-01/label/rh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01/label/rh.BA1_exvivo.label freesurfer-7.1.1/sub-01/label/rh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01/label/rh.BA2_exvivo.label @@ -455,23 +458,14 @@ freesurfer-7.1.1/sub-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01/label/rh.MT_exvivo.label -freesurfer-7.1.1/sub-01/label/rh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01/label/rh.V1_exvivo.label -freesurfer-7.1.1/sub-01/label/rh.V1_exvivo.thresh.label 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+nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3.nii.gz nipype-1.8.0/sub-01/anatomical_pipeline/pypeline.log nipype-1.8.0/sub-01/eeg_pipeline/d3.js nipype-1.8.0/sub-01/eeg_pipeline/eeg_check_input/_inputs.pklz @@ -842,9 +842,9 @@ nipype-1.8.0/sub-01/eeg_pipeline/eeg_datasource/_inputs.pklz nipype-1.8.0/sub-01/eeg_pipeline/eeg_datasource/_node.pklz nipype-1.8.0/sub-01/eeg_pipeline/eeg_datasource/_report/report.rst nipype-1.8.0/sub-01/eeg_pipeline/eeg_datasource/result_eeg_datasource.pklz +nipype-1.8.0/sub-01/eeg_pipeline/graph1.json nipype-1.8.0/sub-01/eeg_pipeline/graph.dot nipype-1.8.0/sub-01/eeg_pipeline/graph.json nipype-1.8.0/sub-01/eeg_pipeline/graph.svg -nipype-1.8.0/sub-01/eeg_pipeline/graph1.json nipype-1.8.0/sub-01/eeg_pipeline/index.html nipype-1.8.0/sub-01/eeg_pipeline/pypeline.log From ae98f7266c6794e74e41020d368edd5c27860c67 Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 16:35:06 +0200 Subject: [PATCH 19/26] [upd] Update test08 --- .../ds-sample_test-08_outputs.txt | 303 ++++++++++++------ 1 file changed, 212 insertions(+), 91 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt index b6cb1e63..4e6e8daf 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-08_outputs.txt @@ -1,10 +1,31 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json @@ -16,11 +37,47 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-brain_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-CSF_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_timeseries.mat 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+cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_timeseries.npy +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_timeseries.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_timeseries.npy +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_timeseries.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_timeseries.npy +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_meanBOLD.nii.gz +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_motion.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-bandpass_bold.nii.gz cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.json cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_fMRI_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -50,19 +107,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label @@ -94,19 +146,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label @@ -115,10 +162,9 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz +freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -138,7 +184,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -147,16 +192,28 @@ freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log.bak freesurfer-7.1.1/sub-01_ses-01/mri/norm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/nu.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/orig/001.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig_nu.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rh.ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/segment.dat -freesurfer-7.1.1/sub-01_ses-01/mri/surface.defects.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/talairach.label_intensities.txt @@ -171,14 +228,12 @@ freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm -freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt -freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log @@ -190,10 +245,7 @@ freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.local-copy freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.log freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log -freesurfer-7.1.1/sub-01_ses-01/scripts/recon-config.yaml -freesurfer-7.1.1/sub-01_ses-01/scripts/unknown-args.txt freesurfer-7.1.1/sub-01_ses-01/stats/aseg.stats -freesurfer-7.1.1/sub-01_ses-01/stats/brainvol.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.a2009s.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.pial.stats @@ -211,8 +263,6 @@ freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -222,7 +272,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -230,8 +279,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.BE.crv @@ -262,7 +310,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/rh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.K @@ -270,8 +317,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm.BE.crv @@ -293,7 +339,16 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.white freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.K +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.Lausanne2018.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.a2009s2aseg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.DKTatlas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/apas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/asegmerge.touch freesurfer-7.1.1/sub-01_ses-01/touch/ca_label.touch @@ -310,26 +365,25 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.pctsurfcon.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.pial_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.qsphere.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphmorph.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphreg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.surfvolume.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.tessellate.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.topofix.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.H.K.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.preaparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.white_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/nu.touch freesurfer-7.1.1/sub-01_ses-01/touch/relabelhypos.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc2.touch @@ -337,31 +391,43 @@ freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.pctsurfcon.touch 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+nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale5_dseg_flirt.mat +nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale5_dseg_flirt.nii.gz nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/eroded_wm_registered.nii.gz From 4ad3c7694d00a03dfa8c169dd4d4e2f5f3a08e00 Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 16:39:25 +0200 Subject: [PATCH 20/26] [upd] Update test07 --- .../ds-sample_test-07_outputs.txt | 312 +++++++++++++----- 1 file changed, 221 insertions(+), 91 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt index 154d1778..5562b7ec 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt @@ -1,10 +1,31 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json @@ -16,11 +37,51 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-CSF_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_desc-eroded_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-meanBOLD_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_timeseries.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale1_timeseries.npy +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_timeseries.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale2_timeseries.npy +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_timeseries.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale3_timeseries.npy +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_timeseries.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale4_timeseries.npy +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.graphml +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_timeseries.mat +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_atlas-L2018_res-scale5_timeseries.npy +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_meanBOLD.nii.gz +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_motion.tsv +cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-bandpass_bold.nii.gz cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.json cmp-v3.2.0/sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-cmp_bold.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_fMRI_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -50,19 +111,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label @@ -94,19 +150,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label @@ -115,10 +166,9 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz +freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -138,7 +188,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -147,16 +196,28 @@ freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log.bak freesurfer-7.1.1/sub-01_ses-01/mri/norm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/nu.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/orig/001.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig_nu.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rh.ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz 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freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/talairach.label_intensities.txt @@ -171,14 +232,12 @@ freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm -freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt -freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log @@ -190,10 +249,7 @@ freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.local-copy freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.log freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log -freesurfer-7.1.1/sub-01_ses-01/scripts/recon-config.yaml -freesurfer-7.1.1/sub-01_ses-01/scripts/unknown-args.txt freesurfer-7.1.1/sub-01_ses-01/stats/aseg.stats -freesurfer-7.1.1/sub-01_ses-01/stats/brainvol.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.a2009s.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.pial.stats @@ -211,8 +267,6 @@ freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -222,7 +276,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -230,8 +283,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.BE.crv @@ -262,7 +314,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/rh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.K @@ -270,8 +321,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm.BE.crv @@ -293,7 +343,16 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.white freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.K +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.Lausanne2018.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.a2009s2aseg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.DKTatlas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/apas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/asegmerge.touch freesurfer-7.1.1/sub-01_ses-01/touch/ca_label.touch @@ -310,26 +369,25 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate2.touch 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freesurfer-7.1.1/sub-01_ses-01/touch/relabelhypos.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc2.touch @@ -337,31 +395,43 @@ freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.pctsurfcon.touch 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nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/command.txt nipype-1.8.0/sub-01/ses-01/fMRI_pipeline/registration_stage/apply_registration_wm_eroded/eroded_wm_registered.nii.gz From 614bb31f627eb0e736588f4df8badf80e775c4c2 Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 16:43:06 +0200 Subject: [PATCH 21/26] [upd] Update test03 --- .../ds-sample_test-03_outputs.txt | 372 +++++++++--------- 1 file changed, 186 insertions(+), 186 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt index 5c4f19fa..b09991ce 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-03_outputs.txt @@ -1,52 +1,52 @@ cmp-custom/dataset_description.json -cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv -cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv -cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv -cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz -cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz +cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz +cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-custom/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-custom/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz @@ -68,21 +68,23 @@ cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json cmp-v3.2.0/sub-01/ses-01/xfm/sub-01_ses-01_space-DWI_desc-head_T1w.mat freesurfer-7.1.1/dataset_description.json -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab -freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz -freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab +freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.label @@ -103,20 +105,20 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA2_exvivo.label @@ -137,40 +139,21 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz +freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.mgz @@ -179,18 +162,18 @@ freesurfer-7.1.1/sub-01_ses-01/mri/aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.presurf.hypos.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.presurf.mgz freesurfer-7.1.1/sub-01_ses-01/mri/brain.finalsurfs.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/brain.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/brain.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/brainmask.auto.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/brainmask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/brainmask.mgz freesurfer-7.1.1/sub-01_ses-01/mri/brainmask.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/brainmask_eroded.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/brain.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/brain.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/lh.ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log @@ -203,51 +186,68 @@ freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rh.ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz 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-freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.stats -freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats -freesurfer-7.1.1/sub-01_ses-01/stats/rh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.aparc.a2009s.stats +freesurfer-7.1.1/sub-01_ses-01/stats/rh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.aparc.pial.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.aparc.stats +freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.stats +freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats @@ -274,11 +274,11 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.BE.crv freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.C.crv freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.FI.crv freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.H.crv -freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.K.crv 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+nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_threshold_brainmask/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_threshold_brainmask/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_threshold_brainmask/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_threshold_brainmask/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_threshold_brainmask/brain_mask.nii.gz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_threshold_brainmask/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_threshold_brainmask/result_mr_threshold_brainmask.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/mrtrix_5tt.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/command.txt -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/mrtrix_5tt.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mrtrix_5tt/result_mrtrix_5tt.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/ROIs_resample/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/ROIs_resample/_node.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/ROIs_resample/_report/report.rst +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/ROIs_resample/result_ROIs_resample.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/result_wm_mask_resample.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/wm_mask_resample/wm_mask_resampled.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/pypeline.log @@ -877,29 +877,29 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registrat nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_roivs/result_apply_registration_roivs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale1_dseg_out_flirt.mat nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_roivs/sub-01_ses-01_atlas-L2018_res-scale1_dseg_out_flirt.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_wm/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_wm/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_wm/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_wm/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_wm/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_wm/result_apply_registration_wm.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_wm/wm_mask_registered.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_registration_wm/wm_mask_resampled_flirt.mat +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/extract_first/command.txt +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/extract_first/first.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/extract_first/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/extract_first/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/extract_first/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/extract_first/command.txt -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/extract_first/first.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/extract_first/result_extract_first.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/T1-TO-TARGET.mat -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/T1-TO-TARGET.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/result_linear_registration.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/T1-TO-TARGET.mat +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/linear_registration/T1-TO-TARGET.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/target_resample/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/target_resample/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/target_resample/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/target_resample/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/target_resample/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/target_resample/result_target_resample.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/target_resample/target_first.nii.gz From 7e2c6e0d961f3cb6c2f225c44cf2d3f2a85a1812 Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 16:52:09 +0200 Subject: [PATCH 22/26] [upd] Update test05 --- .../ds-sample_test-05_outputs.txt | 298 ++++++++++++------ 1 file changed, 209 insertions(+), 89 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt index da374479..0f7718be 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt @@ -1,10 +1,31 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json @@ -16,13 +37,45 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-CSF_probseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GM_probseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_probseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt +cmp-v3.2.0/sub-01/ses-01/xfm/final0GenericAffine.mat +cmp-v3.2.0/sub-01/ses-01/xfm/final1Warp.nii.gz freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -52,19 +105,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label @@ -96,19 +144,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label @@ -117,10 +160,9 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz +freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -140,7 +182,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -149,16 +190,28 @@ freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log.bak freesurfer-7.1.1/sub-01_ses-01/mri/norm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/nu.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/orig/001.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig_nu.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rh.ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/segment.dat -freesurfer-7.1.1/sub-01_ses-01/mri/surface.defects.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/talairach.label_intensities.txt @@ -173,14 +226,12 @@ freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm -freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt -freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log @@ -192,10 +243,7 @@ freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.local-copy freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.log freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log -freesurfer-7.1.1/sub-01_ses-01/scripts/recon-config.yaml -freesurfer-7.1.1/sub-01_ses-01/scripts/unknown-args.txt freesurfer-7.1.1/sub-01_ses-01/stats/aseg.stats -freesurfer-7.1.1/sub-01_ses-01/stats/brainvol.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.a2009s.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.pial.stats @@ -213,8 +261,6 @@ freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -224,7 +270,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -232,8 +277,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.BE.crv @@ -264,7 +308,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/rh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.K @@ -272,8 +315,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm.BE.crv @@ -295,7 +337,16 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.white freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.K +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.Lausanne2018.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.a2009s2aseg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.DKTatlas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/apas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/asegmerge.touch freesurfer-7.1.1/sub-01_ses-01/touch/ca_label.touch @@ -312,26 +363,25 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch 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+nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/final_fiberslength_scale3.npy +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/final_fiberslength_scale4.npy +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/final_fiberslength_scale5.npy nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/result_compute_matrice.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/compute_matrice/streamline_final.trk nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/merge_additional_maps/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/merge_additional_maps/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/connectome_stage/merge_additional_maps/_report/report.rst @@ -468,6 +576,10 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/dipy_dete nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/dipy_deterministic_tracking/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/dipy_deterministic_tracking/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/dipy_deterministic_tracking/result_dipy_deterministic_tracking.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasinker/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasinker/_node.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasinker/_report/report.rst +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasinker/result_dwi_datasinker.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasource/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasource/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasource/_report/report.rst @@ -764,7 +876,11 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/result_mr_convert_roi_volumes.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-Desikan_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_T1/anat.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_T1/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_T1/_inputs.pklz @@ -840,7 +956,11 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roiv nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/result_apply_warp_roivs.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-Desikan_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale1_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale2_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale3_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale4_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale5_dseg_out_warped.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_T1/anat_resampled_warped.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_T1/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_T1/_inputs.pklz From 8ba2f59658d3fd6e97822a03ee8c7358cf02ff17 Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 17:19:16 +0200 Subject: [PATCH 23/26] [upd] Update test06 --- .../ds-sample_test-06_outputs.txt | 298 ++++++++++++------ 1 file changed, 209 insertions(+), 89 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt index 2added49..ab8eaa55 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-06_outputs.txt @@ -1,10 +1,31 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.graphml -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_dseg.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_FreeSurferColorLUT.txt -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-Desikan_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json @@ -16,13 +37,45 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale1_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale2_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale3_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale4_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_atlas-L2018_res-scale5_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_mask +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-brain_T1w.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_desc-head_T1w.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-CSF_probseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GM_probseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_probseg.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bvec cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-PROB_tractogram.trk +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt +cmp-v3.2.0/sub-01/ses-01/xfm/final0GenericAffine.mat +cmp-v3.2.0/sub-01/ses-01/xfm/final1Warp.nii.gz freesurfer-7.1.1/dataset_description.json freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab @@ -52,19 +105,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label @@ -96,19 +144,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label @@ -117,10 +160,9 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz +freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto_noCCseg.label_intensities.txt @@ -140,7 +182,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/csf_mask.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ctrl_pts.mgz freesurfer-7.1.1/sub-01_ses-01/mri/filled.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/freesurferaparc/ROIv_HR_th.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm_eroded.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/fsmask_1mm.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/gmmask.nii.gz @@ -149,16 +190,28 @@ freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log.bak freesurfer-7.1.1/sub-01_ses-01/mri/norm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/nu.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/orig/001.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig_nu.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rh.ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ribbon.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_freesurferaparc.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/segment.dat -freesurfer-7.1.1/sub-01_ses-01/mri/surface.defects.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/talairach.label_intensities.txt @@ -173,14 +226,12 @@ freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm -freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt -freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log @@ -192,10 +243,7 @@ freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.local-copy freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.log freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log -freesurfer-7.1.1/sub-01_ses-01/scripts/recon-config.yaml -freesurfer-7.1.1/sub-01_ses-01/scripts/unknown-args.txt freesurfer-7.1.1/sub-01_ses-01/stats/aseg.stats -freesurfer-7.1.1/sub-01_ses-01/stats/brainvol.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.a2009s.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.pial.stats @@ -213,8 +261,6 @@ freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -224,7 +270,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -232,8 +277,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.BE.crv @@ -264,7 +308,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/rh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.K @@ -272,8 +315,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm.BE.crv @@ -295,7 +337,16 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.white freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.white.preaparc.K +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.Lausanne2018.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/tmp/aparc+aseg.native.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale1_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.a2009s2aseg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.DKTatlas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/apas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/asegmerge.touch freesurfer-7.1.1/sub-01_ses-01/touch/ca_label.touch @@ -312,26 +363,25 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.pctsurfcon.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.pial_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.qsphere.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphmorph.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphreg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.surfvolume.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.tessellate.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.topofix.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.H.K.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.preaparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.white_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/nu.touch 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nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasource/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasource/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/dwi_datasource/_report/report.rst @@ -763,7 +875,11 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/result_mr_convert_roi_volumes.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-Desikan_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_roi_volumes/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_T1/anat.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_T1/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/preprocessing_stage/mr_convert_T1/_inputs.pklz @@ -839,7 +955,11 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roiv nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/result_apply_warp_roivs.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-Desikan_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale1_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale2_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale3_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale4_dseg_out_warped.nii.gz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_roivs/sub-01_ses-01_atlas-L2018_res-scale5_dseg_out_warped.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_T1/anat_resampled_warped.nii.gz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_T1/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/apply_warp_T1/_inputs.pklz From 29bc1111cbcbf9cd2d67b195e4eb30f78827e3b0 Mon Sep 17 00:00:00 2001 From: emullier Date: Wed, 14 Aug 2024 21:50:53 +0200 Subject: [PATCH 24/26] [upd] update the rest of the circleci test --- .../ds-sample_test-02_outputs.txt | 3 - .../ds-sample_test-04_outputs.txt | 127 +- .../ds-sample_test-09-simg_outputs.txt | 240 ++-- .../ds003505_test-10_outputs.txt | 1239 +++++++++++------ 4 files changed, 989 insertions(+), 620 deletions(-) diff --git a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt index 4bd849df..49161fda 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-02_outputs.txt @@ -393,9 +393,6 @@ nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurf nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/csf_mask.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/fsmask_1mm.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/gmmask.nii.gz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_node.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_report/report.rst -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/result_NativeFreesurfer_parcellation.pklz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_inputs.pklz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_node.pklz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/NativeFreesurfer_parcellation/_report/report.rst diff --git a/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt index 730023c5..c9cf3ccd 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-04_outputs.txt @@ -49,24 +49,14 @@ cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-5TT_probseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-GMWMI_probseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_space-DWI_label-WM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.graphml -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale1_conndata-network_connectivity.tsv cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.graphml -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale2_conndata-network_connectivity.tsv cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.graphml -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale3_conndata-network_connectivity.tsv cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.graphml -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale4_conndata-network_connectivity.tsv cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.gpickle -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.graphml -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.mat cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_atlas-L2018_res-scale5_conndata-network_connectivity.tsv cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-brain_mask.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.bval @@ -75,14 +65,13 @@ cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.json cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-cmp_dwi.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-grad_dwi.txt cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_desc-preproc_dwi.nii.gz -cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-DET_tractogram.trk +cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_desc-PROB_tractogram.trk cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_FOD.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_GFA.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_MSD.nii.gz cmp-v3.2.0/sub-01/ses-01/dwi/sub-01_ses-01_model-SHORE_RTOP.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_diffusion_config.json -cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_log.txt cmp-v3.2.0/sub-01/ses-01/xfm/final0GenericAffine.mat cmp-v3.2.0/sub-01/ses-01/xfm/final1Warp.nii.gz freesurfer-7.1.1/dataset_description.json @@ -114,24 +103,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label @@ -163,24 +142,14 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex+hipamyg.label freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG3.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.FG4.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc1.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc2.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc3v.mpm.vpnl.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.hOc4v.mpm.vpnl.label freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale1.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.mpm.vpnl.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label @@ -189,7 +158,7 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/mri/antsdn.brain.mgz +freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz @@ -219,7 +188,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log freesurfer-7.1.1/sub-01_ses-01/mri/mri_nu_correct.mni.log.bak freesurfer-7.1.1/sub-01_ses-01/mri/norm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/nu.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/orig/001.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig.mgz freesurfer-7.1.1/sub-01_ses-01/mri/orig_nu.mgz freesurfer-7.1.1/sub-01_ses-01/mri/rawavg.mgz @@ -242,7 +210,6 @@ freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz freesurfer-7.1.1/sub-01_ses-01/mri/segment.dat -freesurfer-7.1.1/sub-01_ses-01/mri/surface.defects.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz freesurfer-7.1.1/sub-01_ses-01/mri/talairach.label_intensities.txt @@ -257,14 +224,12 @@ freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.m3z freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_with_skull.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm -freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.xfm.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt freesurfer-7.1.1/sub-01_ses-01/mri/wm.asegedit.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wmparc.mgz freesurfer-7.1.1/sub-01_ses-01/mri/wm.seg.mgz freesurfer-7.1.1/sub-01_ses-01/scripts/build-stamp.txt -freesurfer-7.1.1/sub-01_ses-01/scripts/defect2seg.log freesurfer-7.1.1/sub-01_ses-01/scripts/lastcall.build-stamp.txt freesurfer-7.1.1/sub-01_ses-01/scripts/patchdir.txt freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log @@ -276,10 +241,7 @@ freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.local-copy freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.log freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log -freesurfer-7.1.1/sub-01_ses-01/scripts/recon-config.yaml -freesurfer-7.1.1/sub-01_ses-01/scripts/unknown-args.txt freesurfer-7.1.1/sub-01_ses-01/stats/aseg.stats -freesurfer-7.1.1/sub-01_ses-01/stats/brainvol.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.a2009s.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.DKTatlas.stats freesurfer-7.1.1/sub-01_ses-01/stats/lh.aparc.pial.stats @@ -297,8 +259,6 @@ freesurfer-7.1.1/sub-01_ses-01/stats/rh.BA_exvivo.thresh.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.curv.stats freesurfer-7.1.1/sub-01_ses-01/stats/rh.w-g.pct.stats freesurfer-7.1.1/sub-01_ses-01/stats/wmparc.stats -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.lh.dat -freesurfer-7.1.1/sub-01_ses-01/surf/autodet.gw.stats.rh.dat freesurfer-7.1.1/sub-01_ses-01/surf/lh.area freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.mid freesurfer-7.1.1/sub-01_ses-01/surf/lh.area.pial @@ -308,7 +268,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/lh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/lh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.K @@ -316,8 +275,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/lh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/lh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/lh.pial freesurfer-7.1.1/sub-01_ses-01/surf/lh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.BE.crv @@ -348,7 +306,6 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.curv.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_borders freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_chull freesurfer-7.1.1/sub-01_ses-01/surf/rh.defect_labels -freesurfer-7.1.1/sub-01_ses-01/surf/rh.defects.pointset freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.H freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.K @@ -356,8 +313,7 @@ freesurfer-7.1.1/sub-01_ses-01/surf/rh.inflated.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.jacobian_white freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.nofix -freesurfer-7.1.1/sub-01_ses-01/surf/rh.orig.premesh -freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial.T1 +freesurfer-7.1.1/sub-01_ses-01/surf/rh.pial freesurfer-7.1.1/sub-01_ses-01/surf/rh.qsphere.nofix freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm freesurfer-7.1.1/sub-01_ses-01/surf/rh.smoothwm.BE.crv @@ -387,6 +343,8 @@ freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale2_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale3_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale4_Lausanne2018.nii.gz freesurfer-7.1.1/sub-01_ses-01/tmp/ROI_scale5_Lausanne2018.nii.gz +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.a2009s2aseg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/aparc.DKTatlas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/apas2aseg.touch freesurfer-7.1.1/sub-01_ses-01/touch/asegmerge.touch freesurfer-7.1.1/sub-01_ses-01/touch/ca_label.touch @@ -403,26 +361,25 @@ freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.pctsurfcon.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.pial_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.qsphere.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm1.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.smoothwm2.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphmorph.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.sphreg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.surfvolume.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.tessellate.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.topofix.touch freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.H.K.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.preaparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/lh.white.touch +freesurfer-7.1.1/sub-01_ses-01/touch/lh.white_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/nu.touch freesurfer-7.1.1/sub-01_ses-01/touch/relabelhypos.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc2.touch @@ -430,31 +387,43 @@ freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats3.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparcstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.aparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.autodet.gw.stats.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.avgcurv.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex+hipamyg.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.cortex.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.curvstats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.final_surfaces.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate1.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.inflate.H.K.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.jacobian_white.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.pctsurfcon.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.pial_surface.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.qsphere.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.smoothwm1.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.smoothwm2.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.sphmorph.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.sphreg.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.surfvolume.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.tessellate.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.topofix.touch freesurfer-7.1.1/sub-01_ses-01/touch/rh.white.H.K.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.white.preaparc.touch -freesurfer-7.1.1/sub-01_ses-01/touch/rh.white.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rh.white_surface.touch +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_ca_register.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_em_register.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_em_register.skull.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_fix_topology.lh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_fix_topology.rh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_inflate.lh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_inflate.rh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_register.lh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_register.rh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_sphere.lh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mris_sphere.rh.dat +freesurfer-7.1.1/sub-01_ses-01/touch/rusage.mri_watershed.dat freesurfer-7.1.1/sub-01_ses-01/touch/segstats.touch freesurfer-7.1.1/sub-01_ses-01/touch/skull.lta.touch freesurfer-7.1.1/sub-01_ses-01/touch/skull_strip.touch freesurfer-7.1.1/sub-01_ses-01/touch/talairach.touch freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.stats.touch +freesurfer-7.1.1/sub-01_ses-01/touch/wmaparc.touch freesurfer-7.1.1/sub-01_ses-01/touch/wmsegment.touch nipype-1.8.0/dataset_description.json nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/anat_datasinker/_inputs.pklz @@ -532,40 +501,15 @@ nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/R nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3_dil.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3.nii.gz nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/pypeline.log -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/segmentation_stage/copyOrig/_node.pklz 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+nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/mrtrix_probabilistic_tracking/command.txt +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/mrtrix_probabilistic_tracking/_inputs.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/mrtrix_probabilistic_tracking/_node.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/mrtrix_probabilistic_tracking/_report/report.rst +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/mrtrix_probabilistic_tracking/result_mrtrix_probabilistic_tracking.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/mrtrix_probabilistic_tracking/shore_fodf_tracked.tck nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/sift_node/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/sift_node/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/sift_node/_node.pklz @@ -640,11 +584,6 @@ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/trackvis/ nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/trackvis/_node.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/trackvis/_report/report.rst nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/trackvis/result_trackvis.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/voxel2WorldMatrixExtracter/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/voxel2WorldMatrixExtracter/_node.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/voxel2WorldMatrixExtracter/_report/report.rst -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/voxel2WorldMatrixExtracter/result_voxel2WorldMatrixExtracter.pklz -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/voxel2WorldMatrixExtracter/voxel2world.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/wm_erode/command.txt nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/wm_erode/_inputs.pklz nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/diffusion_stage/tracking/wm_erode/_node.pklz diff --git a/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt index 35c5965a..566809a3 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-09-simg_outputs.txt @@ -1,50 +1,52 @@ cmp-v3.2.0/dataset_description.json -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale1_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale2_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale3_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale4_stats.tsv -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.graphml cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_dseg.tsv +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_FreeSurferColorLUT.txt cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_atlas-L2018_res-scale5_stats.tsv cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aparcaseg_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-aseg_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_mask.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.json cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-cmp_T1w.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_desc-head_T1w.nii.gz +cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-CSF_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-GM_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-WM_dseg.nii.gz -cmp-v3.2.0/sub-01/ses-01/anat/sub-01_ses-01_label-brain_desc-eroded_dseg.nii.gz cmp-v3.2.0/sub-01/ses-01/sub-01_ses-01_anatomical_config.json freesurfer-7.1.1/dataset_description.json -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab -freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab -freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz -freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.a2009s.ctab freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.ctab +freesurfer-7.1.1/sub-01_ses-01/label/aparc.annot.DKTatlas.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.ctab +freesurfer-7.1.1/sub-01_ses-01/label/BA_exvivo.thresh.ctab +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA2_exvivo.label @@ -65,15 +67,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.a2009s.annot -freesurfer-7.1.1/sub-01_ses-01/label/lh.aparc.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.entorhinal_exvivo.thresh.label @@ -82,8 +75,17 @@ freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale3.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale4.annot freesurfer-7.1.1/sub-01_ses-01/label/lh.lausanne2018.scale5.annot +freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/lh.perirhinal_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.V1_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/lh.V2_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA1_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA2_exvivo.label @@ -104,15 +106,6 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA6_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.BA_exvivo.thresh.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.DKTatlas.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.a2009s.annot -freesurfer-7.1.1/sub-01_ses-01/label/rh.aparc.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.cortex.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.entorhinal_exvivo.thresh.label @@ -121,28 +114,18 @@ freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale2.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale3.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale4.annot freesurfer-7.1.1/sub-01_ses-01/label/rh.lausanne2018.scale5.annot +freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.MT_exvivo.thresh.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.label freesurfer-7.1.1/sub-01_ses-01/label/rh.perirhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale1_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale2_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale3_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale4_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROI_scale5_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale1_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale2_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale3_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale4_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.ni.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/ROIv_scale5_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01_ses-01/mri/T1.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz +freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.V1_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.label +freesurfer-7.1.1/sub-01_ses-01/label/rh.V2_exvivo.thresh.label +freesurfer-7.1.1/sub-01_ses-01/label/T1w_class-GM.nii.gz +freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aparc.DKTatlas+aseg.mgz -freesurfer-7.1.1/sub-01_ses-01/mri/aparc.a2009s+aseg.mgz freesurfer-7.1.1/sub-01_ses-01/mri/aseg.auto.mgz 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+nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ROIv_Lausanne2018_scale5_final.nii.gz +nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ROIv_Lausanne2018_scale5_FreeSurferColorLUT.txt +nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ROIv_Lausanne2018_scale5.graphml +nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3_dil.nii.gz +nipype-1.8.0/sub-01/anatomical_pipeline/parcellation_stage/parcCombiner/ventricle3.nii.gz +nipype-1.8.0/sub-01/anatomical_pipeline/pypeline.log +nipype-1.8.0/sub-01/eeg_pipeline/eeg_check_input/_inputs.pklz +nipype-1.8.0/sub-01/eeg_pipeline/eeg_check_input/_node.pklz +nipype-1.8.0/sub-01/eeg_pipeline/eeg_check_input/_report/report.rst +nipype-1.8.0/sub-01/eeg_pipeline/eeg_check_input/result_eeg_check_input.pklz From 86fdacbbcb6469575cd215293823fa1b8d2ec450 Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 4 Feb 2025 11:01:33 +0100 Subject: [PATCH 25/26] [fix] update environment.yml --- docker/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/environment.yml b/docker/environment.yml index 216e67cf..a1842b67 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -9,7 +9,7 @@ dependencies: - python=3.8 - pip=20.1.1 - ants=2.2.0 -- numpy=1.21.0 +- numpy=1.23.5 - matplotlib=3.2.2 - graphviz=2.40.1 - traits=6.2.0 From 2fde4227c63396e6c5889503dabe30b4c8a3bea1 Mon Sep 17 00:00:00 2001 From: emullier Date: Tue, 4 Feb 2025 11:03:48 +0100 Subject: [PATCH 26/26] [fix] update environment.yml conda --- conda/environment.yml | 2 +- docker/environment.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conda/environment.yml b/conda/environment.yml index 960c021f..2295ab9b 100644 --- a/conda/environment.yml +++ b/conda/environment.yml @@ -18,7 +18,7 @@ dependencies: - pyqt5-sip=12.9.0 - pip: - - numpy==1.21.6 + - numpy==1.23.5 - matplotlib==3.5.2 - configparser==5.2.0 - nibabel==3.2.2 diff --git a/docker/environment.yml b/docker/environment.yml index a1842b67..216e67cf 100644 --- a/docker/environment.yml +++ b/docker/environment.yml @@ -9,7 +9,7 @@ dependencies: - python=3.8 - pip=20.1.1 - ants=2.2.0 -- numpy=1.23.5 +- numpy=1.21.0 - matplotlib=3.2.2 - graphviz=2.40.1 - traits=6.2.0