├── .github └── workflows │ └── ci.yml ├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── addons └── COMMIT-Filter │ ├── COMMIT_script.py │ ├── README.md │ └── commit_filter.m ├── make.template ├── make_functional.m ├── make_structural.m ├── src ├── anatomical_steps │ ├── collect_region_properties.m │ └── parcellation.m ├── functional_pipeline │ ├── compute_motion_metrics.m │ ├── config_functional_default.json │ ├── functionalParameterProperties.xlsx │ ├── functional_pipeline.m │ ├── functional_preprocessing.m │ ├── load_nifti_fmri.m │ └── reconstruction_functional_network.m ├── functional_preprocessing │ └── preprocess_default.sh ├── misc │ ├── checkParams.m │ ├── freesurfer_scripts │ │ ├── copyright_notice.txt │ │ ├── fsgettmppath.m │ │ ├── load_nifti.m │ │ ├── load_nifti_hdr.m │ │ ├── load_nifti_partially.m │ │ ├── read_annotation.m │ │ ├── save_nifti.m │ │ ├── strlen.m │ │ └── write_annotation.m │ ├── list2struct.m │ ├── load_gtab.m │ ├── load_nifti_hdr_fast.m │ ├── nifti_orientation.m │ ├── parseConfigParams.m │ ├── parseVarargin.m │ ├── prettyjson.m │ ├── readColorLookupTable.m │ ├── readConfigFile.m │ ├── readTrk.m │ ├── saveConfigFile.m │ ├── setup_environment.m │ ├── setup_environment.sh │ ├── struct2list.m │ ├── trackvis_tools │ │ ├── createTrkHeader.m │ │ ├── readTrkHeader.m │ │ └── writeTrkHeader.m │ ├── updateParameters.m │ └── updateStatus.m ├── structural_pipeline │ ├── Preprocessing │ │ └── structural_preprocessing.m │ ├── Reconstruction-Diffusion │ │ ├── csd │ │ │ ├── auto_response.m │ │ │ ├── cart2sphere.m │ │ │ ├── copyright_notice.txt │ │ │ ├── csd_data │ │ │ │ └── sphere_small.txt │ │ │ ├── csdeconv.m │ │ │ ├── estimate_response.m │ │ │ ├── real_sph_harm.m │ │ │ ├── reconstruction_basis │ │ │ │ ├── faces.txt │ │ │ │ └── reconstruction_basis.txt │ │ │ ├── sph_harm_ind_list.m │ │ │ └── srcsd.m │ │ ├── dti │ │ │ ├── iRESTORE.m │ │ │ ├── lmsolverDTI.m │ │ │ ├── tensor2measure.m │ │ │ ├── tensor2peak.m │ │ │ └── thresholdAssistant.m │ │ ├── gqi │ │ │ ├── gqi.m │ │ │ └── reconstruction_basis │ │ │ │ ├── faces.txt │ │ │ │ └── reconstruction_basis.txt │ │ └── reconstruction_diffusion.m │ ├── Reconstruction-Fiber-Properties │ │ ├── getFiberPropertiesFromFile.m │ │ └── reconstruction_fiber_properties.m │ ├── Reconstruction-Fibers │ │ ├── FACT.m │ │ ├── reconstruction_fibers.m │ │ └── writeFibers.m │ ├── Reconstruction-Network │ │ └── reconstruction_network.m │ ├── config_structural_default.json │ ├── structuralParameterProperties.xlsx │ └── structural_pipeline.m ├── structural_preprocessing │ ├── preprocess_eddy.sh │ ├── preprocess_minimal.sh │ └── preprocess_topup_eddy.sh └── templates │ ├── BB50human │ ├── BB50human.annot.ctab │ ├── ROIs_BB50human.txt │ ├── lh.BB50human.gcs │ ├── parcellate_BB50human.sh │ └── rh.BB50human.gcs │ ├── aparc │ ├── ROIs_aparc.txt │ ├── aparc.annot.ctab │ └── parcellate_aparc.sh │ ├── economo │ ├── ROIs_economo.txt │ ├── economo.annot.ctab │ ├── lh.economo.gcs │ ├── parcellate_economo.sh │ └── rh.economo.gcs │ ├── lausanne120 │ ├── ROIs_lausanne120.txt │ ├── lausanne120.annot.ctab │ ├── lh.lausanne120.gcs │ ├── parcellate_lausanne120.sh │ └── rh.lausanne120.gcs │ ├── lausanne250 │ ├── ROIs_lausanne250.txt │ ├── lausanne250.annot.ctab │ ├── lh.lausanne250.gcs │ ├── parcellate_lausanne250.sh │ └── rh.lausanne250.gcs │ └── lausanne500 │ ├── ROIs_lausanne500.txt │ ├── lausanne500.annot.ctab │ ├── lh.lausanne500.gcs │ ├── parcellate_lausanne500.sh │ └── rh.lausanne500.gcs └── tests ├── assets └── template_nifti.nii.gz ├── config_SC_ref.json ├── functional_pipeline ├── misc │ └── simulate_functional_data.m ├── test_functional_pipeline.m └── test_reconstruction_functional_network.m ├── run_testSuite.m └── structural_pipeline ├── misc ├── SimulateDWMRI │ ├── SimulateDWMRI │ │ ├── DEMO_SimulateDWMRI_field.m │ │ ├── DEMO_SimulateDWMRI_voxel.m │ │ ├── README.txt │ │ ├── SimulateDWMRI.m │ │ ├── plotDTI.m │ │ └── writeFDT.m │ └── license.txt ├── anglePeaks.m ├── 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