release/v3.2.0

.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

.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
+    }
+
+}
+

.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
+    }
+}
+
+

.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
+  }
+
+
+
+}