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 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"], + "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": "Probabilistic", + "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": "Probabilistic", + "mrtrix_tracking_config.use_act": true, + "mrtrix_tracking_config.cutoff_value": 0.05, + "mrtrix_tracking_config.backtrack": true, + "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": true, + "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": 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 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..566809a3 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-01_outputs.txt @@ -1,50 +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 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 @@ -151,18 +134,18 @@ 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 @@ -175,51 +158,68 @@ 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 +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/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 freesurfer-7.1.1/sub-01_ses-01/mri/talairach.log freesurfer-7.1.1/sub-01_ses-01/mri/talairach_with_skull.log freesurfer-7.1.1/sub-01_ses-01/mri/transforms/cc_up.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.auto.xfm freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.auto.xfm.lta -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.xfm freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_avi.log freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach_avi_QA.log +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/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/wm.seg.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/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 freesurfer-7.1.1/sub-01_ses-01/scripts/pctsurfcon.log.old freesurfer-7.1.1/sub-01_ses-01/scripts/ponscc.cut.log -freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all-status.log freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.cmd freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.done freesurfer-7.1.1/sub-01_ses-01/scripts/recon-all.env 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-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 @@ -246,11 +246,11 @@ 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 freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.K1.crv freesurfer-7.1.1/sub-01_ses-01/surf/lh.smoothwm.K2.crv 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-nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/_inputs.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/_node.pklz -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/_report/report.rst -nipype-1.8.0/sub-01/ses-01/anatomical_pipeline/parcellation_stage/parcCombiner/result_parcCombiner.pklz -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/parcellation_stage/parcCombiner/ROIv_Lausanne2018_scale5_FreeSurferColorLUT.txt +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 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..49161fda 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 +1,31 @@ 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 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 +46,20 @@ 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 @@ -78,42 +80,22 @@ 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 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-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_freesurferaparc.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+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 @@ -122,19 +104,19 @@ 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/freesurferaparc/ROIv_HR_th.nii.gz 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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 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 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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 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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-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 @@ -65,22 +65,24 @@ 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/dwi/sub-01_ses-01_model-SHORE_desc-PROB_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 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 @@ -101,15 +103,6 @@ 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 @@ -118,8 +111,17 @@ 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 @@ -140,15 +142,6 @@ 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 @@ -157,28 +150,18 @@ 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 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 @@ -187,18 +170,18 @@ 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 @@ -211,51 +194,68 @@ 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 +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/T1.mgz +freesurfer-7.1.1/sub-01_ses-01/mri/T1.nii.gz 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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/command.txt -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/fa_corrected_unmasked.mif 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-05_outputs.txt b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt index e63e3cac..0f7718be 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-05_outputs.txt @@ -1,49 +1,49 @@ 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-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-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 @@ -67,22 +67,24 @@ 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/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 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 @@ -103,15 +105,6 @@ 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 @@ -120,8 +113,17 @@ 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 @@ -142,15 +144,6 @@ 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 @@ -159,28 +152,18 @@ 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 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 @@ -189,18 +172,18 @@ 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 @@ -213,51 +196,68 @@ 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 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-nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA/fa_corrected.mif nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA/result_tensor2FA.pklz +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/command.txt +nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/fa_corrected_unmasked.mif 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/command.txt -nipype-1.8.0/sub-01/ses-01/diffusion_pipeline/registration_stage/tensor2FA_unmasked/fa_corrected_unmasked.mif 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 56272baa..5562b7ec 100644 --- a/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt +++ b/.circleci/tests/expected_outputs/ds-sample_test-07_outputs.txt @@ -1,42 +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 @@ -83,12 +83,14 @@ 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 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 @@ -109,15 +111,6 @@ 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 @@ -126,8 +119,17 @@ 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 @@ -148,15 +150,6 @@ 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 @@ -165,28 +158,18 @@ 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 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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 @@ -79,12 +79,14 @@ 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 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 @@ -105,15 +107,6 @@ 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 @@ -122,8 +115,17 @@ 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 @@ -144,15 +146,6 @@ 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 @@ -161,28 +154,18 @@ 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 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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 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 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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_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 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 @@ -151,18 +134,18 @@ 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 @@ -175,51 +158,68 @@ 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 +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/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 freesurfer-7.1.1/sub-01_ses-01/mri/talairach.log freesurfer-7.1.1/sub-01_ses-01/mri/talairach_with_skull.log freesurfer-7.1.1/sub-01_ses-01/mri/transforms/cc_up.lta freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.auto.xfm freesurfer-7.1.1/sub-01_ses-01/mri/transforms/talairach.auto.xfm.lta -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.xfm 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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 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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 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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 -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 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freesurfer-7.1.1/sub-01/mri/transforms/talairach.xfm freesurfer-7.1.1/sub-01/mri/transforms/talairach.xfm.lta -freesurfer-7.1.1/sub-01/mri/transforms/talairach_avi.log -freesurfer-7.1.1/sub-01/mri/transforms/talairach_avi_QA.log -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 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+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 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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 +freesurfer-7.1.1/fsaverage/label/rh.PALS_B12.labels.gii freesurfer-7.1.1/fsaverage/label/rh.PALS_B12_Lobes.annot freesurfer-7.1.1/fsaverage/label/rh.PALS_B12_OrbitoFrontal.annot freesurfer-7.1.1/fsaverage/label/rh.PALS_B12_Visuotopic.annot +freesurfer-7.1.1/fsaverage/label/rh.perirhinal_exvivo.label +freesurfer-7.1.1/fsaverage/label/rh.perirhinal_exvivo.thresh.label freesurfer-7.1.1/fsaverage/label/rh.V1_exvivo.label freesurfer-7.1.1/fsaverage/label/rh.V1_exvivo.thresh.label 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 -freesurfer-7.1.1/fsaverage/label/rh.high-myelin.label -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.perirhinal_exvivo.label -freesurfer-7.1.1/fsaverage/label/rh.perirhinal_exvivo.thresh.label -freesurfer-7.1.1/fsaverage/mri.2mm/README -freesurfer-7.1.1/fsaverage/mri.2mm/T1.mgz +freesurfer-7.1.1/fsaverage/label/Yeo_Brainmap_fsaverage_README freesurfer-7.1.1/fsaverage/mri.2mm/aseg.mgz -freesurfer-7.1.1/fsaverage/mri.2mm/brain.mgz 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 -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 -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 -freesurfer-7.1.1/sub-01/label/rh.V2_exvivo.label -freesurfer-7.1.1/sub-01/label/rh.V2_exvivo.thresh.label -freesurfer-7.1.1/sub-01/label/rh.aparc.DKTatlas.annot -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.cortex+hipamyg.label freesurfer-7.1.1/sub-01/label/rh.cortex.label freesurfer-7.1.1/sub-01/label/rh.entorhinal_exvivo.label freesurfer-7.1.1/sub-01/label/rh.entorhinal_exvivo.thresh.label +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.hOc1.mpm.vpnl.label freesurfer-7.1.1/sub-01/label/rh.hOc2.mpm.vpnl.label freesurfer-7.1.1/sub-01/label/rh.hOc3v.mpm.vpnl.label @@ -482,29 +476,18 @@ freesurfer-7.1.1/sub-01/label/rh.lausanne2018.scale3.annot freesurfer-7.1.1/sub-01/label/rh.lausanne2018.scale4.annot freesurfer-7.1.1/sub-01/label/rh.lausanne2018.scale5.annot freesurfer-7.1.1/sub-01/label/rh.mpm.vpnl.annot +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.perirhinal_exvivo.label freesurfer-7.1.1/sub-01/label/rh.perirhinal_exvivo.thresh.label -freesurfer-7.1.1/sub-01/mri/ROI_scale1_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01/mri/ROI_scale2_Lausanne2018.nii.gz -freesurfer-7.1.1/sub-01/mri/ROI_scale3_Lausanne2018.nii.gz 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datalad-neuroimaging==0.3.1 pybids==0.14.0