├── .editorconfig ├── .git-blame-ignore-rev ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── discussion.md │ ├── feature_request.md │ └── question.md ├── PULL_REQUEST_TEMPLATE │ └── pull_request_template.md ├── dependabot.yaml └── workflows │ ├── build_and_deploy.yml │ ├── lint.yaml │ ├── publish.yaml │ ├── stale.yaml │ ├── test.yml │ ├── test_converters.yml │ ├── test_instantiation.yml │ ├── test_non_regression_fast.yml │ ├── test_pipelines_anat.yml │ ├── test_pipelines_anat_freesurfer.yml │ ├── test_pipelines_dwi.yml │ ├── test_pipelines_dwi_preprocessing.yml │ └── test_pipelines_pet.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE.txt ├── Makefile ├── README.md ├── clinica ├── __init__.py ├── cmdline.py ├── compat.py ├── converters │ ├── __init__.py │ ├── _utils.py │ ├── abstract_converter.py │ ├── adni_to_bids │ │ ├── __init__.py │ │ ├── _converter.py │ │ ├── _json.py │ │ ├── _utils.py │ │ ├── cli.py │ │ ├── modality_converters │ │ │ ├── __init__.py │ │ │ ├── _av45_fbb_pet.py │ │ │ ├── _dwi.py │ │ │ ├── _factory.py │ │ │ ├── _fdg_pet.py │ │ │ ├── _flair.py │ │ │ ├── _fmap.py │ │ │ ├── _fmri.py │ │ │ ├── _image_path_utils.py │ │ │ ├── _path_to_bids.py │ │ │ ├── _pet_utils.py │ │ │ ├── _pib_pet.py │ │ │ ├── _qc_utils.py │ │ │ ├── _t1.py │ │ │ ├── _tau_pet.py │ │ │ └── _visits_utils.py │ │ └── specifications │ │ │ ├── participant.tsv │ │ │ ├── scans.tsv │ │ │ └── sessions.tsv │ ├── aibl_to_bids │ │ ├── __init__.py │ │ ├── _converter.py │ │ ├── cli.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── bids.py │ │ │ ├── clinical.py │ │ │ └── json.py │ ├── cli.py │ ├── cli_param.py │ ├── factory.py │ ├── genfi_to_bids │ │ ├── __init__.py │ │ ├── _converter.py │ │ ├── _utils.py │ │ ├── cli.py │ │ ├── data.tsv │ │ ├── data_mapping.tsv │ │ └── specifications.csv │ ├── habs_to_bids │ │ ├── __init__.py │ │ ├── _converter.py │ │ └── cli.py │ ├── ixi_to_bids │ │ ├── __init__.py │ │ ├── _converter.py │ │ ├── _utils.py │ │ ├── cli.py │ │ └── dwi_b_files │ │ │ ├── bvals.txt │ │ │ └── bvecs.txt │ ├── nifd_to_bids │ │ ├── __init__.py │ │ ├── _converter.py │ │ ├── _utils.py │ │ └── cli.py │ ├── oasis3_to_bids │ │ ├── __init__.py │ │ ├── _converter.py │ │ ├── _utils.py │ │ └── cli.py │ ├── oasis_to_bids │ │ ├── __init__.py │ │ ├── _converter.py │ │ ├── _utils.py │ │ └── cli.py │ ├── specifications │ │ ├── participant.tsv │ │ ├── scans.tsv │ │ └── sessions.tsv │ ├── study_models.py │ └── ukb_to_bids │ │ ├── __init__.py │ │ ├── _converter.py │ │ ├── _utils.py │ │ ├── cli.py │ │ └── specifications.csv ├── dataset │ ├── __init__.py │ ├── _dataset_type.py │ ├── _versioning.py │ ├── _visit.py │ ├── bids │ │ ├── __init__.py │ │ ├── _dataset_description.py │ │ ├── _filename.py │ │ ├── _queries.py │ │ ├── _readme.py │ │ └── _validation.py │ └── caps │ │ ├── __init__.py │ │ ├── _dataset_description.py │ │ └── _validation.py ├── engine │ ├── __init__.py │ ├── cmdparser.py │ └── template.py ├── iotools │ ├── __init__.py │ ├── center_nifti.py │ ├── cli.py │ ├── data_handling │ │ ├── __init__.py │ │ ├── _centering.py │ │ ├── _files.py │ │ ├── _merging.py │ │ ├── _missing.py │ │ └── _missing_modality_tracker.py │ ├── describe.py │ ├── merge_tsv.py │ └── pipeline_handling.py ├── option.py ├── pipelines │ ├── __init__.py │ ├── anatomical │ │ ├── __init__.py │ │ └── freesurfer │ │ │ ├── __init__.py │ │ │ ├── atlas │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ ├── info.json │ │ │ ├── pipeline.py │ │ │ ├── tasks.py │ │ │ └── utils.py │ │ │ ├── longitudinal │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ ├── correction │ │ │ │ ├── __init__.py │ │ │ │ ├── cli.py │ │ │ │ ├── info.json │ │ │ │ ├── pipeline.py │ │ │ │ ├── tasks.py │ │ │ │ └── utils.py │ │ │ ├── template │ │ │ │ ├── __init__.py │ │ │ │ ├── cli.py │ │ │ │ ├── info.json │ │ │ │ ├── pipeline.py │ │ │ │ ├── tasks.py │ │ │ │ └── utils.py │ │ │ └── utils.py │ │ │ ├── t1 │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ ├── info.json │ │ │ ├── pipeline.py │ │ │ ├── tasks.py │ │ │ ├── utils.py │ │ │ └── visualizer.py │ │ │ └── utils.py │ ├── cli.py │ ├── cli_param │ │ ├── __init__.py │ │ ├── argument.py │ │ ├── option.py │ │ └── option_group.py │ ├── deeplearning_prepare_data │ │ ├── __init__.py │ │ └── deeplearning_prepare_data_cli.py │ ├── dwi │ │ ├── __init__.py │ │ ├── connectome │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ ├── info.json │ │ │ ├── pipeline.py │ │ │ ├── tasks.py │ │ │ └── utils.py │ │ ├── dti │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ ├── info.json │ │ │ ├── pipeline.py │ │ │ ├── tasks.py │ │ │ └── utils.py │ │ ├── preprocessing │ │ │ ├── __init__.py │ │ │ ├── engine.py │ │ │ ├── fmap │ │ │ │ ├── __init__.py │ │ │ │ ├── cli.py │ │ │ │ ├── info.json │ │ │ │ ├── pipeline.py │ │ │ │ ├── tasks.py │ │ │ │ ├── utils.py │ │ │ │ └── workflows.py │ │ │ ├── t1 │ │ │ │ ├── __init__.py │ │ │ │ ├── cli.py │ │ │ │ ├── info.json │ │ │ │ ├── pipeline.py │ │ │ │ ├── tasks.py │ │ │ │ ├── utils.py │ │ │ │ └── workflows.py │ │ │ ├── tasks.py │ │ │ ├── utils.py │ │ │ └── workflows.py │ │ └── utils.py │ ├── engine.py │ ├── machine_learning │ │ ├── __init__.py │ │ ├── algorithm.py │ │ ├── base.py │ │ ├── classification_cli.py │ │ ├── input.py │ │ ├── ml_utils.py │ │ ├── ml_workflows.py │ │ ├── region_based_io.py │ │ ├── tsv_based_io.py │ │ ├── validation.py │ │ ├── vertex_based_io.py │ │ └── voxel_based_io.py │ ├── machine_learning_spatial_svm │ │ ├── __init__.py │ │ ├── info.json │ │ ├── spatial_svm_cli.py │ │ ├── spatial_svm_pipeline.py │ │ └── spatial_svm_utils.py │ ├── pet │ │ ├── __init__.py │ │ ├── engine.py │ │ ├── linear │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ ├── info.json │ │ │ ├── pipeline.py │ │ │ ├── tasks.py │ │ │ └── utils.py │ │ ├── utils.py │ │ └── volume │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ ├── info.json │ │ │ ├── pipeline.py │ │ │ ├── tasks.py │ │ │ └── utils.py │ ├── pet_surface │ │ ├── __init__.py │ │ ├── applyInverseDeformationField.m │ │ ├── info.json │ │ ├── pet_surface_cli.py │ │ ├── pet_surface_longitudinal_cli.py │ │ ├── pet_surface_pipeline.py │ │ └── pet_surface_utils.py │ ├── statistics_surface │ │ ├── __init__.py │ │ ├── _utils.py │ │ ├── cli.py │ │ ├── info.json │ │ ├── pipeline.py │ │ └── surfstat │ │ │ ├── __init__.py │ │ │ ├── _surfstat.py │ │ │ ├── _utils.py │ │ │ └── models │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── _contrast.py │ │ │ ├── _correlation.py │ │ │ ├── _factory.py │ │ │ ├── _group.py │ │ │ ├── _utils.py │ │ │ └── results │ │ │ ├── __init__.py │ │ │ ├── _base.py │ │ │ ├── _plot.py │ │ │ ├── _serialize.py │ │ │ └── _statistics.py │ ├── statistics_volume │ │ ├── __init__.py │ │ ├── info.json │ │ ├── statistics_volume_cli.py │ │ ├── statistics_volume_pipeline.py │ │ ├── statistics_volume_utils.py │ │ ├── template_model_contrast.m │ │ ├── template_model_creation.m │ │ ├── template_model_estimation.m │ │ └── template_model_results.m │ ├── statistics_volume_correction │ │ ├── __init__.py │ │ ├── info.json │ │ ├── statistics_volume_correction_cli.py │ │ ├── statistics_volume_correction_pipeline.py │ │ └── statistics_volume_correction_utils.py │ ├── t1_linear │ │ ├── __init__.py │ │ ├── anat_linear_pipeline.py │ │ ├── anat_linear_utils.py │ │ ├── flair_linear_cli.py │ │ ├── info.json │ │ ├── t1_linear_cli.py │ │ └── tasks.py │ ├── t1_volume │ │ ├── __init__.py │ │ ├── info.json │ │ └── t1_volume_cli.py │ ├── t1_volume_create_dartel │ │ ├── __init__.py │ │ ├── info.json │ │ ├── t1_volume_create_dartel_cli.py │ │ └── t1_volume_create_dartel_pipeline.py │ ├── t1_volume_dartel2mni │ │ ├── __init__.py │ │ ├── info.json │ │ ├── t1_volume_dartel2mni_cli.py │ │ ├── t1_volume_dartel2mni_pipeline.py │ │ └── t1_volume_dartel2mni_utils.py │ ├── t1_volume_existing_template │ │ ├── __init__.py │ │ ├── info.json │ │ └── t1_volume_existing_template_cli.py │ ├── t1_volume_parcellation │ │ ├── __init__.py │ │ ├── info.json │ │ ├── t1_volume_parcellation_cli.py │ │ ├── t1_volume_parcellation_pipeline.py │ │ └── t1_volume_parcellation_utils.py │ ├── t1_volume_register_dartel │ │ ├── __init__.py │ │ ├── info.json │ │ ├── t1_volume_register_dartel_cli.py │ │ ├── t1_volume_register_dartel_pipeline.py │ │ └── t1_volume_register_dartel_utils.py │ ├── t1_volume_tissue_segmentation │ │ ├── __init__.py │ │ ├── info.json │ │ ├── t1_volume_tissue_segmentation_cli.py │ │ ├── t1_volume_tissue_segmentation_pipeline.py │ │ └── t1_volume_tissue_segmentation_utils.py │ └── tasks.py ├── pydra │ ├── __init__.py │ ├── dwi │ │ ├── __init__.py │ │ └── _commons │ │ │ ├── __init__.py │ │ │ ├── _tasks.py │ │ │ └── _workflows.py │ ├── engine.py │ ├── engine_utils.py │ ├── interfaces.py │ ├── machine_learning_spatial_svm │ │ ├── __init__.py │ │ ├── pipeline.py │ │ ├── spatial_svm_cli.py │ │ └── tasks.py │ ├── pet_linear │ │ ├── __init__.py │ │ ├── pet_linear_cli.py │ │ ├── pipeline.py │ │ └── tasks.py │ ├── pet_volume │ │ ├── __init__.py │ │ ├── pet_volume_cli.py │ │ ├── pipeline.py │ │ └── tasks.py │ ├── query.py │ ├── shared_workflows │ │ ├── __init__.py │ │ └── smoothing.py │ ├── statistics_volume │ │ ├── __init__.py │ │ ├── pipeline.py │ │ ├── statistics_volume_cli.py │ │ └── task.py │ ├── statistics_volume_correction │ │ ├── __init__.py │ │ ├── pipeline.py │ │ ├── statistics_volume_correction_cli.py │ │ └── task.py │ ├── t1_freesurfer │ │ ├── __init__.py │ │ ├── cli.py │ │ ├── pipeline.py │ │ └── tasks.py │ ├── t1_linear │ │ ├── __init__.py │ │ ├── t1_linear.py │ │ └── t1_linear_cli.py │ ├── t1_volume │ │ ├── __init__.py │ │ ├── create_dartel │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ └── pipeline.py │ │ ├── dartel2mni │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ ├── pipeline.py │ │ │ └── tasks.py │ │ ├── register_dartel │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ └── pipeline.py │ │ ├── tasks.py │ │ ├── tissue_segmentation │ │ │ ├── __init__.py │ │ │ ├── cli.py │ │ │ └── pipeline.py │ │ └── utils.py │ ├── tasks │ │ ├── __init__.py │ │ ├── parsers.py │ │ ├── readers.py │ │ ├── templates.py │ │ └── writers.py │ └── utils.py ├── resources │ ├── atlases │ │ ├── atlas-AAL2.txt │ │ ├── atlas-AAL2_dseg.nii.gz │ │ ├── atlas-AAL2_dseg.tsv │ │ ├── atlas-AICHA.txt │ │ ├── atlas-AICHA_dseg.nii.gz │ │ ├── atlas-AICHA_dseg.tsv │ │ ├── atlas-Hammers_dseg.tsv │ │ ├── atlas-JHUDTI81_dseg.tsv │ │ ├── atlas-JHUTract_dseg.tsv │ │ ├── atlas-LPBA40_dseg.tsv │ │ └── atlas-Neuromorphometrics_dseg.tsv │ ├── fmri │ │ └── task-facesshapesemotion_events.tsv │ ├── label_conversion_gtmsegmentation.csv │ ├── mappings │ │ └── .emptyfile │ ├── masks │ │ ├── dilated_MNI_binary_mask.nii.gz │ │ ├── region-cerebellumPons_eroded-6mm_mask.nii.gz │ │ ├── region-cerebellumPons_remove-extrabrain_eroded-3it_mask.nii.gz │ │ ├── region-pons_eroded-6mm_mask.nii.gz │ │ └── region-pons_remove-extrabrain_eroded-2it_mask.nii.gz │ └── templates │ │ └── pipeline_template │ │ ├── README.md.j2 │ │ ├── __init__.py.j2 │ │ ├── cli.py.j2 │ │ ├── info.json.j2 │ │ ├── pipeline.py.j2 │ │ ├── utils.py.j2 │ │ └── visualizer.py.j2 └── utils │ ├── __init__.py │ ├── atlas.py │ ├── check_dependency.py │ ├── dwi.py │ ├── exceptions.py │ ├── filemanip.py │ ├── group.py │ ├── image.py │ ├── input_files.py │ ├── inputs.py │ ├── longitudinal.py │ ├── nipype.py │ ├── participant.py │ ├── pet.py │ ├── spm.py │ ├── statistics.py │ ├── stream.py │ ├── testing_utils.py │ └── ux.py ├── docs ├── Atlases.md ├── BIDS.md ├── CAPS │ ├── Introduction.md │ └── Specifications.md ├── CHANGELOG.md ├── Conferences │ ├── neuro_openscience_workshop_2019.md │ ├── neuro_openscience_workshop_2023.md │ └── ohbm_2018.md ├── Converters │ ├── ADNI2BIDS.md │ ├── AIBL2BIDS.md │ ├── GENFItoBIDS.md │ ├── HABS2BIDS.md │ ├── IXItoBIDS.md │ ├── NIFD2BIDS.md │ ├── OASIS2BIDS.md │ ├── OASIS3TOBIDS.md │ └── UKBtoBIDS.md ├── IOTools │ ├── center_nifti.md │ ├── check_missing_modalities.md │ ├── check_missing_processing.md │ ├── create_subjects_visits.md │ ├── describe.md │ └── merge_tsv.md ├── Pipelines │ ├── DWI_Connectome.md │ ├── DWI_DTI.md │ ├── DWI_Preprocessing.md │ ├── FLAIR_Linear.md │ ├── MachineLearning_Classification.md │ ├── MachineLearning_PrepareSVM.md │ ├── PET_Introduction.md │ ├── PET_Linear.md │ ├── PET_Surface.md │ ├── PET_Surface_Longitudinal.md │ ├── PET_Volume.md │ ├── Stats_Surface.md │ ├── Stats_Volume.md │ ├── T1_FreeSurfer.md │ ├── T1_FreeSurfer_Longitudinal.md │ ├── T1_Linear.md │ └── T1_Volume.md ├── PreparingYourData.md ├── Software │ ├── Installation.md │ ├── InteractingWithClinica.md │ ├── Third-party.md │ └── contributing.md ├── WhatIsClinica.md ├── css │ └── clinica.css ├── glossary.md ├── img │ ├── Clinica_Banner.png │ ├── Clinica_Christmas_Banner.png │ ├── Clinica_Partners_Banner.png │ ├── GENFI_download │ │ └── selection.png │ ├── OASIS3_download │ │ ├── add_age.png │ │ ├── add_education.png │ │ ├── add_mr_sessions.png │ │ ├── check_age.png │ │ ├── edit_columns.png │ │ ├── remove_age.png │ │ └── select_education.png │ ├── PET_Surface │ │ ├── PET_Surface.jpg │ │ ├── PET_Surface_File.png │ │ ├── PET_Surface_Freeview.png │ │ └── PET_Surface_SurfStat.png │ ├── StatsSurfStat_images │ │ └── ContrastNegative-CorrectedPValue.jpg │ ├── T1_FreeSurfer │ │ ├── Visu_Freeview.jpg │ │ ├── t1-freesurfer_pipeline1.svg │ │ ├── t1-freesurfer_pipeline2.svg │ │ └── t1-freesurfer_pipeline3.svg │ ├── T1_Volume │ │ ├── ex_Dartel_template_GM.png │ │ ├── ex_GM_MNI_space.png │ │ └── ex_GM_WM_CSF.png │ ├── clinica_icon.png │ ├── clinica_logo.svg │ └── favicon.ico ├── index.md └── snippets │ ├── abbreviations.md │ ├── cmd_inputs.md │ ├── converters_options.md │ ├── inventory_conferences.md │ ├── inventory_converters.md │ ├── inventory_iotools.md │ ├── inventory_pipelines.md │ ├── known_issues.md │ ├── pipelines_options.md │ ├── spm_banner.md │ └── support.md ├── environment.yml ├── ignore_words.txt ├── mkdocs.yml ├── poetry.lock ├── pyproject.toml └── test ├── __init__.py ├── conftest.py ├── instantiation ├── test_cli.py └── test_instantiate_all_pipelines.py ├── nonregression ├── __init__.py ├── pipelines │ ├── anat │ │ ├── test_t1_freesurfer.py │ │ ├── test_t1_linear.py │ │ └── test_t1_volume.py │ ├── dwi │ │ ├── preprocessing │ │ │ ├── test_phase_diff.py │ │ │ └── test_t1.py │ │ └── test_pipelines.py │ ├── pet │ │ ├── test_pet_linear.py │ │ ├── test_pet_surface.py │ │ └── test_pet_volume.py │ ├── test_run_pipelines_ml.py │ └── test_run_pipelines_stats.py ├── test_run_converters.py ├── test_run_iotools.py └── testing_tools.py └── unittests ├── converters ├── adni_to_bids │ ├── data │ │ ├── ADNI_123_S_4567_template.xml │ │ ├── ADNI_234_S_5678_template.xml │ │ └── ADNI_345_S_6789_template.xml │ ├── modality_converters │ │ ├── test_adni_fmap.py │ │ ├── test_fdg_pet.py │ │ └── test_visits_utils.py │ ├── test_adni_json.py │ └── test_adni_utils.py ├── aibl_to_bids │ ├── test_aibl_json.py │ └── test_aibl_utils.py ├── test_converter_utils.py ├── test_genfi_to_bids_utils.py ├── test_ixi_to_bids_utils.py ├── test_oasis_to_bids_utils.py ├── test_study_models.py └── test_ukb_to_bids_utils.py ├── dataset ├── bids │ ├── test_bids_queries.py │ └── test_bids_validation.py ├── caps │ ├── test_caps_dataset_description.py │ └── test_caps_validation.py └── test_dataset_type.py ├── iotools ├── test_center_nifti.py ├── test_data_handling.py ├── test_describe.py ├── test_iotools_cli.py └── test_pipeline_handling.py ├── pipelines ├── anatomical │ └── freesurfer │ │ ├── atlas │ │ └── test_t1_freesurfer_atlas_pipeline.py │ │ ├── longitudinal │ │ ├── correction │ │ │ └── test_t1_freesurfer_longitudinal_correction_pipeline.py │ │ └── template │ │ │ └── test_t1_freesurfer_longitudinal_template_pipeline.py │ │ ├── t1 │ │ ├── test_t1_freesurfer_pipeline.py │ │ └── test_t1_freesurfer_utils.py │ │ └── test_freesurfer_utils.py ├── dwi │ ├── connectome │ │ └── test_dwi_connectome_pipeline.py │ ├── dti │ │ └── test_dwi_dti_pipeline.py │ ├── preprocessing │ │ ├── test_common_preprocessing_utils.py │ │ ├── test_dwi_preprocessing_using_fmap_pipeline.py │ │ ├── test_dwi_preprocessing_using_t1_pipeline.py │ │ ├── test_fmap_utils.py │ │ └── test_t1_utils.py │ ├── test_common_dwi_utils.py │ └── test_connectome_utils.py ├── pet │ ├── test_pet_linear_pipeline.py │ ├── test_pet_linear_utils.py │ ├── test_pet_volume_pipeline.py │ └── test_pet_volume_utils.py ├── statistics_surface │ ├── data │ │ └── subjects.tsv │ ├── test_inputs.py │ └── test_model.py ├── statistics_volume │ └── test_statistics_volume_utils.py ├── t1_linear │ ├── test_anat_linear_pipeline.py │ └── test_anat_linear_utils.py ├── t1_volume_create_dartel │ └── test_t1_volume_create_dartel_pipeline.py ├── t1_volume_dartel2mni │ └── test_t1_volume_dartel2mni_pipeline.py ├── t1_volume_parcellation │ └── test_t1_volume_parcellation_pipeline.py ├── t1_volume_register_dartel │ └── test_t1_volume_register_dartel_pipeline.py ├── t1_volume_tissue_segmentation │ └── test_t1_volume_tissue_segmentation_pipeline.py └── test_nipype_engine.py ├── pydra ├── t1_volume │ └── dartel2mni │ │ └── test_tasks.py ├── test_engine.py ├── test_interfaces.py ├── test_query.py └── test_utils.py ├── test_testing_tools.py └── utils ├── test_atlas.py ├── test_check_dependency.py ├── test_filemanip.py ├── test_group.py ├── test_image.py ├── test_input_files.py ├── test_longitudinal.py ├── test_nipype.py ├── test_participant.py ├── test_pet.py ├── test_spm.py ├── test_stream.py ├── test_testing_utils.py ├── test_utils_inputs.py └── test_ux.py /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.editorconfig -------------------------------------------------------------------------------- /.git-blame-ignore-rev: -------------------------------------------------------------------------------- 1 | # Migrate code style to Black 2 | 1c4ee4110cb87a1940d103bf09ad653fec747b1b 3 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/ISSUE_TEMPLATE/bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/discussion.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/ISSUE_TEMPLATE/discussion.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/ISSUE_TEMPLATE/feature_request.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/question.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/ISSUE_TEMPLATE/question.md -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE/pull_request_template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md -------------------------------------------------------------------------------- /.github/dependabot.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/dependabot.yaml -------------------------------------------------------------------------------- /.github/workflows/build_and_deploy.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/build_and_deploy.yml -------------------------------------------------------------------------------- /.github/workflows/lint.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/lint.yaml -------------------------------------------------------------------------------- /.github/workflows/publish.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/publish.yaml -------------------------------------------------------------------------------- /.github/workflows/stale.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/stale.yaml -------------------------------------------------------------------------------- /.github/workflows/test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/test.yml -------------------------------------------------------------------------------- /.github/workflows/test_converters.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/test_converters.yml -------------------------------------------------------------------------------- /.github/workflows/test_instantiation.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/test_instantiation.yml -------------------------------------------------------------------------------- /.github/workflows/test_non_regression_fast.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/test_non_regression_fast.yml -------------------------------------------------------------------------------- /.github/workflows/test_pipelines_anat.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/test_pipelines_anat.yml -------------------------------------------------------------------------------- /.github/workflows/test_pipelines_anat_freesurfer.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/test_pipelines_anat_freesurfer.yml -------------------------------------------------------------------------------- /.github/workflows/test_pipelines_dwi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/test_pipelines_dwi.yml -------------------------------------------------------------------------------- /.github/workflows/test_pipelines_dwi_preprocessing.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/test_pipelines_dwi_preprocessing.yml -------------------------------------------------------------------------------- /.github/workflows/test_pipelines_pet.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.github/workflows/test_pipelines_pet.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/CITATION.cff -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/README.md -------------------------------------------------------------------------------- /clinica/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/__init__.py -------------------------------------------------------------------------------- /clinica/cmdline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/cmdline.py -------------------------------------------------------------------------------- /clinica/compat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/compat.py -------------------------------------------------------------------------------- /clinica/converters/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/__init__.py -------------------------------------------------------------------------------- /clinica/converters/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/_utils.py -------------------------------------------------------------------------------- /clinica/converters/abstract_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/abstract_converter.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/__init__.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/_converter.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/_json.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/_utils.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/cli.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/__init__.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_av45_fbb_pet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_av45_fbb_pet.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_dwi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_dwi.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_factory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_factory.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_fdg_pet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_fdg_pet.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_flair.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_flair.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_fmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_fmap.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_fmri.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_fmri.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_image_path_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_image_path_utils.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_path_to_bids.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_pet_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_pet_utils.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_pib_pet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_pib_pet.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_qc_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_qc_utils.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_t1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_t1.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_tau_pet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_tau_pet.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/modality_converters/_visits_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/modality_converters/_visits_utils.py -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/specifications/participant.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/specifications/participant.tsv -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/specifications/scans.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/specifications/scans.tsv -------------------------------------------------------------------------------- /clinica/converters/adni_to_bids/specifications/sessions.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/adni_to_bids/specifications/sessions.tsv -------------------------------------------------------------------------------- /clinica/converters/aibl_to_bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/aibl_to_bids/__init__.py -------------------------------------------------------------------------------- /clinica/converters/aibl_to_bids/_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/aibl_to_bids/_converter.py -------------------------------------------------------------------------------- /clinica/converters/aibl_to_bids/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/aibl_to_bids/cli.py -------------------------------------------------------------------------------- /clinica/converters/aibl_to_bids/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/aibl_to_bids/utils/__init__.py -------------------------------------------------------------------------------- /clinica/converters/aibl_to_bids/utils/bids.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/aibl_to_bids/utils/bids.py -------------------------------------------------------------------------------- /clinica/converters/aibl_to_bids/utils/clinical.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/aibl_to_bids/utils/clinical.py -------------------------------------------------------------------------------- /clinica/converters/aibl_to_bids/utils/json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/aibl_to_bids/utils/json.py -------------------------------------------------------------------------------- /clinica/converters/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/cli.py -------------------------------------------------------------------------------- /clinica/converters/cli_param.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/cli_param.py -------------------------------------------------------------------------------- /clinica/converters/factory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/factory.py -------------------------------------------------------------------------------- /clinica/converters/genfi_to_bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/genfi_to_bids/__init__.py -------------------------------------------------------------------------------- /clinica/converters/genfi_to_bids/_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/genfi_to_bids/_converter.py -------------------------------------------------------------------------------- /clinica/converters/genfi_to_bids/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/genfi_to_bids/_utils.py -------------------------------------------------------------------------------- /clinica/converters/genfi_to_bids/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/genfi_to_bids/cli.py -------------------------------------------------------------------------------- /clinica/converters/genfi_to_bids/data.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/genfi_to_bids/data.tsv -------------------------------------------------------------------------------- /clinica/converters/genfi_to_bids/data_mapping.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/genfi_to_bids/data_mapping.tsv -------------------------------------------------------------------------------- /clinica/converters/genfi_to_bids/specifications.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/genfi_to_bids/specifications.csv -------------------------------------------------------------------------------- /clinica/converters/habs_to_bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/habs_to_bids/__init__.py -------------------------------------------------------------------------------- /clinica/converters/habs_to_bids/_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/habs_to_bids/_converter.py -------------------------------------------------------------------------------- /clinica/converters/habs_to_bids/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/habs_to_bids/cli.py -------------------------------------------------------------------------------- /clinica/converters/ixi_to_bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ixi_to_bids/__init__.py -------------------------------------------------------------------------------- /clinica/converters/ixi_to_bids/_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ixi_to_bids/_converter.py -------------------------------------------------------------------------------- /clinica/converters/ixi_to_bids/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ixi_to_bids/_utils.py -------------------------------------------------------------------------------- /clinica/converters/ixi_to_bids/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ixi_to_bids/cli.py -------------------------------------------------------------------------------- /clinica/converters/ixi_to_bids/dwi_b_files/bvals.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ixi_to_bids/dwi_b_files/bvals.txt -------------------------------------------------------------------------------- /clinica/converters/ixi_to_bids/dwi_b_files/bvecs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ixi_to_bids/dwi_b_files/bvecs.txt -------------------------------------------------------------------------------- /clinica/converters/nifd_to_bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/nifd_to_bids/__init__.py -------------------------------------------------------------------------------- /clinica/converters/nifd_to_bids/_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/nifd_to_bids/_converter.py -------------------------------------------------------------------------------- /clinica/converters/nifd_to_bids/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/nifd_to_bids/_utils.py -------------------------------------------------------------------------------- /clinica/converters/nifd_to_bids/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/nifd_to_bids/cli.py -------------------------------------------------------------------------------- /clinica/converters/oasis3_to_bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/oasis3_to_bids/__init__.py -------------------------------------------------------------------------------- /clinica/converters/oasis3_to_bids/_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/oasis3_to_bids/_converter.py -------------------------------------------------------------------------------- /clinica/converters/oasis3_to_bids/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/oasis3_to_bids/_utils.py -------------------------------------------------------------------------------- /clinica/converters/oasis3_to_bids/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/oasis3_to_bids/cli.py -------------------------------------------------------------------------------- /clinica/converters/oasis_to_bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/oasis_to_bids/__init__.py -------------------------------------------------------------------------------- /clinica/converters/oasis_to_bids/_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/oasis_to_bids/_converter.py -------------------------------------------------------------------------------- /clinica/converters/oasis_to_bids/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/oasis_to_bids/_utils.py -------------------------------------------------------------------------------- /clinica/converters/oasis_to_bids/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/oasis_to_bids/cli.py -------------------------------------------------------------------------------- /clinica/converters/specifications/participant.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/specifications/participant.tsv -------------------------------------------------------------------------------- /clinica/converters/specifications/scans.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/specifications/scans.tsv -------------------------------------------------------------------------------- /clinica/converters/specifications/sessions.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/specifications/sessions.tsv -------------------------------------------------------------------------------- /clinica/converters/study_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/study_models.py -------------------------------------------------------------------------------- /clinica/converters/ukb_to_bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ukb_to_bids/__init__.py -------------------------------------------------------------------------------- /clinica/converters/ukb_to_bids/_converter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ukb_to_bids/_converter.py -------------------------------------------------------------------------------- /clinica/converters/ukb_to_bids/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ukb_to_bids/_utils.py -------------------------------------------------------------------------------- /clinica/converters/ukb_to_bids/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ukb_to_bids/cli.py -------------------------------------------------------------------------------- /clinica/converters/ukb_to_bids/specifications.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/converters/ukb_to_bids/specifications.csv -------------------------------------------------------------------------------- /clinica/dataset/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/__init__.py -------------------------------------------------------------------------------- /clinica/dataset/_dataset_type.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/_dataset_type.py -------------------------------------------------------------------------------- /clinica/dataset/_versioning.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/_versioning.py -------------------------------------------------------------------------------- /clinica/dataset/_visit.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/_visit.py -------------------------------------------------------------------------------- /clinica/dataset/bids/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/bids/__init__.py -------------------------------------------------------------------------------- /clinica/dataset/bids/_dataset_description.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/bids/_dataset_description.py -------------------------------------------------------------------------------- /clinica/dataset/bids/_filename.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/bids/_filename.py -------------------------------------------------------------------------------- /clinica/dataset/bids/_queries.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/bids/_queries.py -------------------------------------------------------------------------------- /clinica/dataset/bids/_readme.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/bids/_readme.py -------------------------------------------------------------------------------- /clinica/dataset/bids/_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/bids/_validation.py -------------------------------------------------------------------------------- /clinica/dataset/caps/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/caps/__init__.py -------------------------------------------------------------------------------- /clinica/dataset/caps/_dataset_description.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/caps/_dataset_description.py -------------------------------------------------------------------------------- /clinica/dataset/caps/_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/dataset/caps/_validation.py -------------------------------------------------------------------------------- /clinica/engine/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/engine/__init__.py -------------------------------------------------------------------------------- /clinica/engine/cmdparser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/engine/cmdparser.py -------------------------------------------------------------------------------- /clinica/engine/template.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/engine/template.py -------------------------------------------------------------------------------- /clinica/iotools/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/__init__.py -------------------------------------------------------------------------------- /clinica/iotools/center_nifti.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/center_nifti.py -------------------------------------------------------------------------------- /clinica/iotools/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/cli.py -------------------------------------------------------------------------------- /clinica/iotools/data_handling/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/data_handling/__init__.py -------------------------------------------------------------------------------- /clinica/iotools/data_handling/_centering.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/data_handling/_centering.py -------------------------------------------------------------------------------- /clinica/iotools/data_handling/_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/data_handling/_files.py -------------------------------------------------------------------------------- /clinica/iotools/data_handling/_merging.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/data_handling/_merging.py -------------------------------------------------------------------------------- /clinica/iotools/data_handling/_missing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/data_handling/_missing.py -------------------------------------------------------------------------------- /clinica/iotools/data_handling/_missing_modality_tracker.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/data_handling/_missing_modality_tracker.py -------------------------------------------------------------------------------- /clinica/iotools/describe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/describe.py -------------------------------------------------------------------------------- /clinica/iotools/merge_tsv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/merge_tsv.py -------------------------------------------------------------------------------- /clinica/iotools/pipeline_handling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/iotools/pipeline_handling.py -------------------------------------------------------------------------------- /clinica/option.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/option.py -------------------------------------------------------------------------------- /clinica/pipelines/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/__init__.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/__init__.py: -------------------------------------------------------------------------------- 1 | from . import freesurfer 2 | -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/__init__.py: -------------------------------------------------------------------------------- 1 | from . import atlas, longitudinal, t1 2 | -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/atlas/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/atlas/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/atlas/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/atlas/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/atlas/info.json -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/atlas/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/atlas/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/atlas/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/atlas/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/atlas/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/atlas/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli, correction, template 2 | -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/correction/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/correction/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/correction/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/correction/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/correction/info.json -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/correction/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/correction/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/correction/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/correction/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/correction/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/correction/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/template/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/template/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/template/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/template/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/template/info.json -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/template/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/template/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/template/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/template/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/template/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/template/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/longitudinal/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/longitudinal/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/t1/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/t1/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/t1/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/t1/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/t1/info.json -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/t1/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/t1/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/t1/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/t1/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/t1/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/t1/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/t1/visualizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/t1/visualizer.py -------------------------------------------------------------------------------- /clinica/pipelines/anatomical/freesurfer/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/anatomical/freesurfer/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/cli_param/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/cli_param/__init__.py -------------------------------------------------------------------------------- /clinica/pipelines/cli_param/argument.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/cli_param/argument.py -------------------------------------------------------------------------------- /clinica/pipelines/cli_param/option.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/cli_param/option.py -------------------------------------------------------------------------------- /clinica/pipelines/cli_param/option_group.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/cli_param/option_group.py -------------------------------------------------------------------------------- /clinica/pipelines/deeplearning_prepare_data/__init__.py: -------------------------------------------------------------------------------- 1 | from . import deeplearning_prepare_data_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/deeplearning_prepare_data/deeplearning_prepare_data_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/deeplearning_prepare_data/deeplearning_prepare_data_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/__init__.py: -------------------------------------------------------------------------------- 1 | from . import connectome, dti, preprocessing 2 | -------------------------------------------------------------------------------- /clinica/pipelines/dwi/connectome/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/dwi/connectome/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/connectome/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/connectome/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/connectome/info.json -------------------------------------------------------------------------------- /clinica/pipelines/dwi/connectome/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/connectome/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/connectome/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/connectome/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/connectome/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/connectome/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/dti/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/dwi/dti/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/dti/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/dti/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/dti/info.json -------------------------------------------------------------------------------- /clinica/pipelines/dwi/dti/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/dti/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/dti/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/dti/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/dti/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/dti/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/__init__.py: -------------------------------------------------------------------------------- 1 | from . import fmap, t1 2 | -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/engine.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/fmap/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/fmap/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/fmap/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/fmap/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/fmap/info.json -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/fmap/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/fmap/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/fmap/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/fmap/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/fmap/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/fmap/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/fmap/workflows.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/fmap/workflows.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/t1/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/t1/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/t1/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/t1/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/t1/info.json -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/t1/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/t1/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/t1/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/t1/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/t1/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/t1/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/t1/workflows.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/t1/workflows.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/preprocessing/workflows.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/preprocessing/workflows.py -------------------------------------------------------------------------------- /clinica/pipelines/dwi/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/dwi/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/engine.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/__init__.py: -------------------------------------------------------------------------------- 1 | from . import classification_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/algorithm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/algorithm.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/base.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/classification_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/classification_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/input.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/ml_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/ml_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/ml_workflows.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/ml_workflows.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/region_based_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/region_based_io.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/tsv_based_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/tsv_based_io.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/validation.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/vertex_based_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/vertex_based_io.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning/voxel_based_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning/voxel_based_io.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning_spatial_svm/__init__.py: -------------------------------------------------------------------------------- 1 | from . import spatial_svm_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning_spatial_svm/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning_spatial_svm/info.json -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning_spatial_svm/spatial_svm_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning_spatial_svm/spatial_svm_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning_spatial_svm/spatial_svm_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning_spatial_svm/spatial_svm_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/machine_learning_spatial_svm/spatial_svm_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/machine_learning_spatial_svm/spatial_svm_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/__init__.py: -------------------------------------------------------------------------------- 1 | from . import linear, volume 2 | -------------------------------------------------------------------------------- /clinica/pipelines/pet/engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/engine.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/linear/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/pet/linear/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/linear/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/linear/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/linear/info.json -------------------------------------------------------------------------------- /clinica/pipelines/pet/linear/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/linear/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/linear/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/linear/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/linear/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/linear/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/volume/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/pet/volume/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/volume/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/volume/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/volume/info.json -------------------------------------------------------------------------------- /clinica/pipelines/pet/volume/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/volume/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/volume/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/volume/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/pet/volume/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet/volume/utils.py -------------------------------------------------------------------------------- /clinica/pipelines/pet_surface/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet_surface/__init__.py -------------------------------------------------------------------------------- /clinica/pipelines/pet_surface/applyInverseDeformationField.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet_surface/applyInverseDeformationField.m -------------------------------------------------------------------------------- /clinica/pipelines/pet_surface/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet_surface/info.json -------------------------------------------------------------------------------- /clinica/pipelines/pet_surface/pet_surface_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet_surface/pet_surface_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/pet_surface/pet_surface_longitudinal_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet_surface/pet_surface_longitudinal_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/pet_surface/pet_surface_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet_surface/pet_surface_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/pet_surface/pet_surface_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/pet_surface/pet_surface_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/cli.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/info.json -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/__init__.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/_surfstat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/_surfstat.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/__init__.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/_base.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/_contrast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/_contrast.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/_correlation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/_correlation.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/_factory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/_factory.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/_group.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/_group.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/results/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/results/__init__.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/results/_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/results/_base.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/results/_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/results/_plot.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/results/_serialize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/results/_serialize.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_surface/surfstat/models/results/_statistics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_surface/surfstat/models/results/_statistics.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume/__init__.py: -------------------------------------------------------------------------------- 1 | from . import statistics_volume_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume/info.json -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume/statistics_volume_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume/statistics_volume_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume/statistics_volume_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume/statistics_volume_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume/statistics_volume_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume/statistics_volume_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume/template_model_contrast.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume/template_model_contrast.m -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume/template_model_creation.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume/template_model_creation.m -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume/template_model_estimation.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume/template_model_estimation.m -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume/template_model_results.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume/template_model_results.m -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume_correction/__init__.py: -------------------------------------------------------------------------------- 1 | from . import statistics_volume_correction_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume_correction/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume_correction/info.json -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume_correction/statistics_volume_correction_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume_correction/statistics_volume_correction_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume_correction/statistics_volume_correction_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume_correction/statistics_volume_correction_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/statistics_volume_correction/statistics_volume_correction_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/statistics_volume_correction/statistics_volume_correction_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_linear/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_linear/__init__.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_linear/anat_linear_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_linear/anat_linear_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_linear/anat_linear_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_linear/anat_linear_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_linear/flair_linear_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_linear/flair_linear_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_linear/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_linear/info.json -------------------------------------------------------------------------------- /clinica/pipelines/t1_linear/t1_linear_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_linear/t1_linear_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_linear/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_linear/tasks.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume/__init__.py: -------------------------------------------------------------------------------- 1 | from . import t1_volume_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume/info.json -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume/t1_volume_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume/t1_volume_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_create_dartel/__init__.py: -------------------------------------------------------------------------------- 1 | from . import t1_volume_create_dartel_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_create_dartel/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_create_dartel/info.json -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_dartel2mni/__init__.py: -------------------------------------------------------------------------------- 1 | from . import t1_volume_dartel2mni_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_dartel2mni/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_dartel2mni/info.json -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_existing_template/__init__.py: -------------------------------------------------------------------------------- 1 | from . import t1_volume_existing_template_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_existing_template/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_existing_template/info.json -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_existing_template/t1_volume_existing_template_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_existing_template/t1_volume_existing_template_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_parcellation/__init__.py: -------------------------------------------------------------------------------- 1 | from . import t1_volume_parcellation_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_parcellation/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_parcellation/info.json -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_register_dartel/__init__.py: -------------------------------------------------------------------------------- 1 | from . import t1_volume_register_dartel_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_register_dartel/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_register_dartel/info.json -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_register_dartel/t1_volume_register_dartel_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_tissue_segmentation/__init__.py: -------------------------------------------------------------------------------- 1 | from . import t1_volume_tissue_segmentation_cli 2 | -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_tissue_segmentation/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_tissue_segmentation/info.json -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_pipeline.py -------------------------------------------------------------------------------- /clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_utils.py -------------------------------------------------------------------------------- /clinica/pipelines/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pipelines/tasks.py -------------------------------------------------------------------------------- /clinica/pydra/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/__init__.py -------------------------------------------------------------------------------- /clinica/pydra/dwi/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /clinica/pydra/dwi/_commons/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/dwi/_commons/__init__.py -------------------------------------------------------------------------------- /clinica/pydra/dwi/_commons/_tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/dwi/_commons/_tasks.py -------------------------------------------------------------------------------- /clinica/pydra/dwi/_commons/_workflows.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/dwi/_commons/_workflows.py -------------------------------------------------------------------------------- /clinica/pydra/engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/engine.py -------------------------------------------------------------------------------- /clinica/pydra/engine_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/engine_utils.py -------------------------------------------------------------------------------- /clinica/pydra/interfaces.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/interfaces.py -------------------------------------------------------------------------------- /clinica/pydra/machine_learning_spatial_svm/__init__.py: -------------------------------------------------------------------------------- 1 | from . import spatial_svm_cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/machine_learning_spatial_svm/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/machine_learning_spatial_svm/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/machine_learning_spatial_svm/spatial_svm_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/machine_learning_spatial_svm/spatial_svm_cli.py -------------------------------------------------------------------------------- /clinica/pydra/machine_learning_spatial_svm/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/machine_learning_spatial_svm/tasks.py -------------------------------------------------------------------------------- /clinica/pydra/pet_linear/__init__.py: -------------------------------------------------------------------------------- 1 | from . import pet_linear_cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/pet_linear/pet_linear_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/pet_linear/pet_linear_cli.py -------------------------------------------------------------------------------- /clinica/pydra/pet_linear/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/pet_linear/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/pet_linear/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/pet_linear/tasks.py -------------------------------------------------------------------------------- /clinica/pydra/pet_volume/__init__.py: -------------------------------------------------------------------------------- 1 | from . import pet_volume_cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/pet_volume/pet_volume_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/pet_volume/pet_volume_cli.py -------------------------------------------------------------------------------- /clinica/pydra/pet_volume/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/pet_volume/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/pet_volume/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/pet_volume/tasks.py -------------------------------------------------------------------------------- /clinica/pydra/query.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/query.py -------------------------------------------------------------------------------- /clinica/pydra/shared_workflows/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /clinica/pydra/shared_workflows/smoothing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/shared_workflows/smoothing.py -------------------------------------------------------------------------------- /clinica/pydra/statistics_volume/__init__.py: -------------------------------------------------------------------------------- 1 | from . import statistics_volume_cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/statistics_volume/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/statistics_volume/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/statistics_volume/statistics_volume_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/statistics_volume/statistics_volume_cli.py -------------------------------------------------------------------------------- /clinica/pydra/statistics_volume/task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/statistics_volume/task.py -------------------------------------------------------------------------------- /clinica/pydra/statistics_volume_correction/__init__.py: -------------------------------------------------------------------------------- 1 | from . import statistics_volume_correction_cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/statistics_volume_correction/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/statistics_volume_correction/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/statistics_volume_correction/statistics_volume_correction_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/statistics_volume_correction/statistics_volume_correction_cli.py -------------------------------------------------------------------------------- /clinica/pydra/statistics_volume_correction/task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/statistics_volume_correction/task.py -------------------------------------------------------------------------------- /clinica/pydra/t1_freesurfer/__init__.py: -------------------------------------------------------------------------------- 1 | from .cli import cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/t1_freesurfer/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_freesurfer/cli.py -------------------------------------------------------------------------------- /clinica/pydra/t1_freesurfer/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_freesurfer/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/t1_freesurfer/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_freesurfer/tasks.py -------------------------------------------------------------------------------- /clinica/pydra/t1_linear/__init__.py: -------------------------------------------------------------------------------- 1 | from . import t1_linear_cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/t1_linear/t1_linear.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_linear/t1_linear.py -------------------------------------------------------------------------------- /clinica/pydra/t1_linear/t1_linear_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_linear/t1_linear_cli.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/__init__.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/create_dartel/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/create_dartel/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/create_dartel/cli.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/create_dartel/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/create_dartel/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/dartel2mni/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/dartel2mni/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/dartel2mni/cli.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/dartel2mni/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/dartel2mni/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/dartel2mni/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/dartel2mni/tasks.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/register_dartel/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/register_dartel/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/register_dartel/cli.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/register_dartel/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/register_dartel/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/tasks.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/tissue_segmentation/__init__.py: -------------------------------------------------------------------------------- 1 | from . import cli 2 | -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/tissue_segmentation/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/tissue_segmentation/cli.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/tissue_segmentation/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/tissue_segmentation/pipeline.py -------------------------------------------------------------------------------- /clinica/pydra/t1_volume/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/t1_volume/utils.py -------------------------------------------------------------------------------- /clinica/pydra/tasks/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/tasks/__init__.py -------------------------------------------------------------------------------- /clinica/pydra/tasks/parsers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/tasks/parsers.py -------------------------------------------------------------------------------- /clinica/pydra/tasks/readers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/tasks/readers.py -------------------------------------------------------------------------------- /clinica/pydra/tasks/templates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/tasks/templates.py -------------------------------------------------------------------------------- /clinica/pydra/tasks/writers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/tasks/writers.py -------------------------------------------------------------------------------- /clinica/pydra/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/pydra/utils.py -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-AAL2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-AAL2.txt -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-AAL2_dseg.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-AAL2_dseg.nii.gz -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-AAL2_dseg.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-AAL2_dseg.tsv -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-AICHA.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-AICHA.txt -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-AICHA_dseg.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-AICHA_dseg.nii.gz -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-AICHA_dseg.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-AICHA_dseg.tsv -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-Hammers_dseg.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-Hammers_dseg.tsv -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-JHUDTI81_dseg.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-JHUDTI81_dseg.tsv -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-JHUTract_dseg.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-JHUTract_dseg.tsv -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-LPBA40_dseg.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-LPBA40_dseg.tsv -------------------------------------------------------------------------------- /clinica/resources/atlases/atlas-Neuromorphometrics_dseg.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/atlases/atlas-Neuromorphometrics_dseg.tsv -------------------------------------------------------------------------------- /clinica/resources/fmri/task-facesshapesemotion_events.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/fmri/task-facesshapesemotion_events.tsv -------------------------------------------------------------------------------- /clinica/resources/label_conversion_gtmsegmentation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/label_conversion_gtmsegmentation.csv -------------------------------------------------------------------------------- /clinica/resources/mappings/.emptyfile: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /clinica/resources/masks/dilated_MNI_binary_mask.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/masks/dilated_MNI_binary_mask.nii.gz -------------------------------------------------------------------------------- /clinica/resources/masks/region-cerebellumPons_eroded-6mm_mask.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/masks/region-cerebellumPons_eroded-6mm_mask.nii.gz -------------------------------------------------------------------------------- /clinica/resources/masks/region-cerebellumPons_remove-extrabrain_eroded-3it_mask.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/masks/region-cerebellumPons_remove-extrabrain_eroded-3it_mask.nii.gz -------------------------------------------------------------------------------- /clinica/resources/masks/region-pons_eroded-6mm_mask.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/masks/region-pons_eroded-6mm_mask.nii.gz -------------------------------------------------------------------------------- /clinica/resources/masks/region-pons_remove-extrabrain_eroded-2it_mask.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/masks/region-pons_remove-extrabrain_eroded-2it_mask.nii.gz -------------------------------------------------------------------------------- /clinica/resources/templates/pipeline_template/README.md.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/templates/pipeline_template/README.md.j2 -------------------------------------------------------------------------------- /clinica/resources/templates/pipeline_template/__init__.py.j2: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /clinica/resources/templates/pipeline_template/cli.py.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/templates/pipeline_template/cli.py.j2 -------------------------------------------------------------------------------- /clinica/resources/templates/pipeline_template/info.json.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/templates/pipeline_template/info.json.j2 -------------------------------------------------------------------------------- /clinica/resources/templates/pipeline_template/pipeline.py.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/templates/pipeline_template/pipeline.py.j2 -------------------------------------------------------------------------------- /clinica/resources/templates/pipeline_template/utils.py.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/templates/pipeline_template/utils.py.j2 -------------------------------------------------------------------------------- /clinica/resources/templates/pipeline_template/visualizer.py.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/resources/templates/pipeline_template/visualizer.py.j2 -------------------------------------------------------------------------------- /clinica/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/__init__.py -------------------------------------------------------------------------------- /clinica/utils/atlas.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/atlas.py -------------------------------------------------------------------------------- /clinica/utils/check_dependency.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/check_dependency.py -------------------------------------------------------------------------------- /clinica/utils/dwi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/dwi.py -------------------------------------------------------------------------------- /clinica/utils/exceptions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/exceptions.py -------------------------------------------------------------------------------- /clinica/utils/filemanip.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/filemanip.py -------------------------------------------------------------------------------- /clinica/utils/group.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/group.py -------------------------------------------------------------------------------- /clinica/utils/image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/image.py -------------------------------------------------------------------------------- /clinica/utils/input_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/input_files.py -------------------------------------------------------------------------------- /clinica/utils/inputs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/inputs.py -------------------------------------------------------------------------------- /clinica/utils/longitudinal.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/longitudinal.py -------------------------------------------------------------------------------- /clinica/utils/nipype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/nipype.py -------------------------------------------------------------------------------- /clinica/utils/participant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/participant.py -------------------------------------------------------------------------------- /clinica/utils/pet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/pet.py -------------------------------------------------------------------------------- /clinica/utils/spm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/spm.py -------------------------------------------------------------------------------- /clinica/utils/statistics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/statistics.py -------------------------------------------------------------------------------- /clinica/utils/stream.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/stream.py -------------------------------------------------------------------------------- /clinica/utils/testing_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/testing_utils.py -------------------------------------------------------------------------------- /clinica/utils/ux.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/clinica/utils/ux.py -------------------------------------------------------------------------------- /docs/Atlases.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Atlases.md -------------------------------------------------------------------------------- /docs/BIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/BIDS.md -------------------------------------------------------------------------------- /docs/CAPS/Introduction.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/CAPS/Introduction.md -------------------------------------------------------------------------------- /docs/CAPS/Specifications.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/CAPS/Specifications.md -------------------------------------------------------------------------------- /docs/CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/CHANGELOG.md -------------------------------------------------------------------------------- /docs/Conferences/neuro_openscience_workshop_2019.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Conferences/neuro_openscience_workshop_2019.md -------------------------------------------------------------------------------- /docs/Conferences/neuro_openscience_workshop_2023.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Conferences/neuro_openscience_workshop_2023.md -------------------------------------------------------------------------------- /docs/Conferences/ohbm_2018.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Conferences/ohbm_2018.md -------------------------------------------------------------------------------- /docs/Converters/ADNI2BIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Converters/ADNI2BIDS.md -------------------------------------------------------------------------------- /docs/Converters/AIBL2BIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Converters/AIBL2BIDS.md -------------------------------------------------------------------------------- /docs/Converters/GENFItoBIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Converters/GENFItoBIDS.md -------------------------------------------------------------------------------- /docs/Converters/HABS2BIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Converters/HABS2BIDS.md -------------------------------------------------------------------------------- /docs/Converters/IXItoBIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Converters/IXItoBIDS.md -------------------------------------------------------------------------------- /docs/Converters/NIFD2BIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Converters/NIFD2BIDS.md -------------------------------------------------------------------------------- /docs/Converters/OASIS2BIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Converters/OASIS2BIDS.md -------------------------------------------------------------------------------- /docs/Converters/OASIS3TOBIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Converters/OASIS3TOBIDS.md -------------------------------------------------------------------------------- /docs/Converters/UKBtoBIDS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Converters/UKBtoBIDS.md -------------------------------------------------------------------------------- /docs/IOTools/center_nifti.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/IOTools/center_nifti.md -------------------------------------------------------------------------------- /docs/IOTools/check_missing_modalities.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/IOTools/check_missing_modalities.md -------------------------------------------------------------------------------- /docs/IOTools/check_missing_processing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/IOTools/check_missing_processing.md -------------------------------------------------------------------------------- /docs/IOTools/create_subjects_visits.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/IOTools/create_subjects_visits.md -------------------------------------------------------------------------------- /docs/IOTools/describe.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/IOTools/describe.md -------------------------------------------------------------------------------- /docs/IOTools/merge_tsv.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/IOTools/merge_tsv.md -------------------------------------------------------------------------------- /docs/Pipelines/DWI_Connectome.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/DWI_Connectome.md -------------------------------------------------------------------------------- /docs/Pipelines/DWI_DTI.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/DWI_DTI.md -------------------------------------------------------------------------------- /docs/Pipelines/DWI_Preprocessing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/DWI_Preprocessing.md -------------------------------------------------------------------------------- /docs/Pipelines/FLAIR_Linear.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/FLAIR_Linear.md -------------------------------------------------------------------------------- /docs/Pipelines/MachineLearning_Classification.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/MachineLearning_Classification.md -------------------------------------------------------------------------------- /docs/Pipelines/MachineLearning_PrepareSVM.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/MachineLearning_PrepareSVM.md -------------------------------------------------------------------------------- /docs/Pipelines/PET_Introduction.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/PET_Introduction.md -------------------------------------------------------------------------------- /docs/Pipelines/PET_Linear.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/PET_Linear.md -------------------------------------------------------------------------------- /docs/Pipelines/PET_Surface.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/PET_Surface.md -------------------------------------------------------------------------------- /docs/Pipelines/PET_Surface_Longitudinal.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/PET_Surface_Longitudinal.md -------------------------------------------------------------------------------- /docs/Pipelines/PET_Volume.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/PET_Volume.md -------------------------------------------------------------------------------- /docs/Pipelines/Stats_Surface.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/Stats_Surface.md -------------------------------------------------------------------------------- /docs/Pipelines/Stats_Volume.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/Stats_Volume.md -------------------------------------------------------------------------------- /docs/Pipelines/T1_FreeSurfer.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/T1_FreeSurfer.md -------------------------------------------------------------------------------- /docs/Pipelines/T1_FreeSurfer_Longitudinal.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/T1_FreeSurfer_Longitudinal.md -------------------------------------------------------------------------------- /docs/Pipelines/T1_Linear.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/T1_Linear.md -------------------------------------------------------------------------------- /docs/Pipelines/T1_Volume.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Pipelines/T1_Volume.md -------------------------------------------------------------------------------- /docs/PreparingYourData.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/PreparingYourData.md -------------------------------------------------------------------------------- /docs/Software/Installation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Software/Installation.md -------------------------------------------------------------------------------- /docs/Software/InteractingWithClinica.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Software/InteractingWithClinica.md -------------------------------------------------------------------------------- /docs/Software/Third-party.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/Software/Third-party.md -------------------------------------------------------------------------------- /docs/Software/contributing.md: -------------------------------------------------------------------------------- 1 | ../../CONTRIBUTING.md -------------------------------------------------------------------------------- /docs/WhatIsClinica.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/WhatIsClinica.md -------------------------------------------------------------------------------- /docs/css/clinica.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/css/clinica.css -------------------------------------------------------------------------------- /docs/glossary.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/glossary.md -------------------------------------------------------------------------------- /docs/img/Clinica_Banner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/Clinica_Banner.png -------------------------------------------------------------------------------- /docs/img/Clinica_Christmas_Banner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/Clinica_Christmas_Banner.png -------------------------------------------------------------------------------- /docs/img/Clinica_Partners_Banner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/Clinica_Partners_Banner.png -------------------------------------------------------------------------------- /docs/img/GENFI_download/selection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/GENFI_download/selection.png -------------------------------------------------------------------------------- /docs/img/OASIS3_download/add_age.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/OASIS3_download/add_age.png -------------------------------------------------------------------------------- /docs/img/OASIS3_download/add_education.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/OASIS3_download/add_education.png -------------------------------------------------------------------------------- /docs/img/OASIS3_download/add_mr_sessions.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/OASIS3_download/add_mr_sessions.png -------------------------------------------------------------------------------- /docs/img/OASIS3_download/check_age.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/OASIS3_download/check_age.png -------------------------------------------------------------------------------- /docs/img/OASIS3_download/edit_columns.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/OASIS3_download/edit_columns.png -------------------------------------------------------------------------------- /docs/img/OASIS3_download/remove_age.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/OASIS3_download/remove_age.png -------------------------------------------------------------------------------- /docs/img/OASIS3_download/select_education.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/OASIS3_download/select_education.png -------------------------------------------------------------------------------- /docs/img/PET_Surface/PET_Surface.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/PET_Surface/PET_Surface.jpg -------------------------------------------------------------------------------- /docs/img/PET_Surface/PET_Surface_File.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/PET_Surface/PET_Surface_File.png -------------------------------------------------------------------------------- /docs/img/PET_Surface/PET_Surface_Freeview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/PET_Surface/PET_Surface_Freeview.png -------------------------------------------------------------------------------- /docs/img/PET_Surface/PET_Surface_SurfStat.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/PET_Surface/PET_Surface_SurfStat.png -------------------------------------------------------------------------------- /docs/img/StatsSurfStat_images/ContrastNegative-CorrectedPValue.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/StatsSurfStat_images/ContrastNegative-CorrectedPValue.jpg -------------------------------------------------------------------------------- /docs/img/T1_FreeSurfer/Visu_Freeview.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/T1_FreeSurfer/Visu_Freeview.jpg -------------------------------------------------------------------------------- /docs/img/T1_FreeSurfer/t1-freesurfer_pipeline1.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/T1_FreeSurfer/t1-freesurfer_pipeline1.svg -------------------------------------------------------------------------------- /docs/img/T1_FreeSurfer/t1-freesurfer_pipeline2.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/T1_FreeSurfer/t1-freesurfer_pipeline2.svg -------------------------------------------------------------------------------- /docs/img/T1_FreeSurfer/t1-freesurfer_pipeline3.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/T1_FreeSurfer/t1-freesurfer_pipeline3.svg -------------------------------------------------------------------------------- /docs/img/T1_Volume/ex_Dartel_template_GM.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/T1_Volume/ex_Dartel_template_GM.png -------------------------------------------------------------------------------- /docs/img/T1_Volume/ex_GM_MNI_space.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/T1_Volume/ex_GM_MNI_space.png -------------------------------------------------------------------------------- /docs/img/T1_Volume/ex_GM_WM_CSF.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/T1_Volume/ex_GM_WM_CSF.png -------------------------------------------------------------------------------- /docs/img/clinica_icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/clinica_icon.png -------------------------------------------------------------------------------- /docs/img/clinica_logo.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/clinica_logo.svg -------------------------------------------------------------------------------- /docs/img/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/img/favicon.ico -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/snippets/abbreviations.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/abbreviations.md -------------------------------------------------------------------------------- /docs/snippets/cmd_inputs.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/cmd_inputs.md -------------------------------------------------------------------------------- /docs/snippets/converters_options.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/converters_options.md -------------------------------------------------------------------------------- /docs/snippets/inventory_conferences.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/inventory_conferences.md -------------------------------------------------------------------------------- /docs/snippets/inventory_converters.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/inventory_converters.md -------------------------------------------------------------------------------- /docs/snippets/inventory_iotools.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/inventory_iotools.md -------------------------------------------------------------------------------- /docs/snippets/inventory_pipelines.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/inventory_pipelines.md -------------------------------------------------------------------------------- /docs/snippets/known_issues.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/known_issues.md -------------------------------------------------------------------------------- /docs/snippets/pipelines_options.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/pipelines_options.md -------------------------------------------------------------------------------- /docs/snippets/spm_banner.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/spm_banner.md -------------------------------------------------------------------------------- /docs/snippets/support.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/docs/snippets/support.md -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/environment.yml -------------------------------------------------------------------------------- /ignore_words.txt: -------------------------------------------------------------------------------- 1 | artic 2 | commun 3 | fo 4 | fwe 5 | nd 6 | siz 7 | te 8 | vox 9 | -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/mkdocs.yml -------------------------------------------------------------------------------- /poetry.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/poetry.lock -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/pyproject.toml -------------------------------------------------------------------------------- /test/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/conftest.py -------------------------------------------------------------------------------- /test/instantiation/test_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/instantiation/test_cli.py -------------------------------------------------------------------------------- /test/instantiation/test_instantiate_all_pipelines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/instantiation/test_instantiate_all_pipelines.py -------------------------------------------------------------------------------- /test/nonregression/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test/nonregression/pipelines/anat/test_t1_freesurfer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/anat/test_t1_freesurfer.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/anat/test_t1_linear.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/anat/test_t1_linear.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/anat/test_t1_volume.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/anat/test_t1_volume.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/dwi/preprocessing/test_phase_diff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/dwi/preprocessing/test_phase_diff.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/dwi/preprocessing/test_t1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/dwi/preprocessing/test_t1.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/dwi/test_pipelines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/dwi/test_pipelines.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/pet/test_pet_linear.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/pet/test_pet_linear.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/pet/test_pet_surface.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/pet/test_pet_surface.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/pet/test_pet_volume.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/pet/test_pet_volume.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/test_run_pipelines_ml.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/test_run_pipelines_ml.py -------------------------------------------------------------------------------- /test/nonregression/pipelines/test_run_pipelines_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/pipelines/test_run_pipelines_stats.py -------------------------------------------------------------------------------- /test/nonregression/test_run_converters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/test_run_converters.py -------------------------------------------------------------------------------- /test/nonregression/test_run_iotools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/test_run_iotools.py -------------------------------------------------------------------------------- /test/nonregression/testing_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/nonregression/testing_tools.py -------------------------------------------------------------------------------- /test/unittests/converters/adni_to_bids/data/ADNI_123_S_4567_template.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/adni_to_bids/data/ADNI_123_S_4567_template.xml -------------------------------------------------------------------------------- /test/unittests/converters/adni_to_bids/data/ADNI_234_S_5678_template.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/adni_to_bids/data/ADNI_234_S_5678_template.xml -------------------------------------------------------------------------------- /test/unittests/converters/adni_to_bids/data/ADNI_345_S_6789_template.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/adni_to_bids/data/ADNI_345_S_6789_template.xml -------------------------------------------------------------------------------- /test/unittests/converters/adni_to_bids/modality_converters/test_adni_fmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/adni_to_bids/modality_converters/test_adni_fmap.py -------------------------------------------------------------------------------- /test/unittests/converters/adni_to_bids/modality_converters/test_fdg_pet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/adni_to_bids/modality_converters/test_fdg_pet.py -------------------------------------------------------------------------------- /test/unittests/converters/adni_to_bids/modality_converters/test_visits_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/adni_to_bids/modality_converters/test_visits_utils.py -------------------------------------------------------------------------------- /test/unittests/converters/adni_to_bids/test_adni_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/adni_to_bids/test_adni_json.py -------------------------------------------------------------------------------- /test/unittests/converters/adni_to_bids/test_adni_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/adni_to_bids/test_adni_utils.py -------------------------------------------------------------------------------- /test/unittests/converters/aibl_to_bids/test_aibl_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/aibl_to_bids/test_aibl_json.py -------------------------------------------------------------------------------- /test/unittests/converters/aibl_to_bids/test_aibl_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/aibl_to_bids/test_aibl_utils.py -------------------------------------------------------------------------------- /test/unittests/converters/test_converter_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/test_converter_utils.py -------------------------------------------------------------------------------- /test/unittests/converters/test_genfi_to_bids_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/test_genfi_to_bids_utils.py -------------------------------------------------------------------------------- /test/unittests/converters/test_ixi_to_bids_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/test_ixi_to_bids_utils.py -------------------------------------------------------------------------------- /test/unittests/converters/test_oasis_to_bids_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/test_oasis_to_bids_utils.py -------------------------------------------------------------------------------- /test/unittests/converters/test_study_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/test_study_models.py -------------------------------------------------------------------------------- /test/unittests/converters/test_ukb_to_bids_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/converters/test_ukb_to_bids_utils.py -------------------------------------------------------------------------------- /test/unittests/dataset/bids/test_bids_queries.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/dataset/bids/test_bids_queries.py -------------------------------------------------------------------------------- /test/unittests/dataset/bids/test_bids_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/dataset/bids/test_bids_validation.py -------------------------------------------------------------------------------- /test/unittests/dataset/caps/test_caps_dataset_description.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/dataset/caps/test_caps_dataset_description.py -------------------------------------------------------------------------------- /test/unittests/dataset/caps/test_caps_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/dataset/caps/test_caps_validation.py -------------------------------------------------------------------------------- /test/unittests/dataset/test_dataset_type.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/dataset/test_dataset_type.py -------------------------------------------------------------------------------- /test/unittests/iotools/test_center_nifti.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/iotools/test_center_nifti.py -------------------------------------------------------------------------------- /test/unittests/iotools/test_data_handling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/iotools/test_data_handling.py -------------------------------------------------------------------------------- /test/unittests/iotools/test_describe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/iotools/test_describe.py -------------------------------------------------------------------------------- /test/unittests/iotools/test_iotools_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/iotools/test_iotools_cli.py -------------------------------------------------------------------------------- /test/unittests/iotools/test_pipeline_handling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/iotools/test_pipeline_handling.py -------------------------------------------------------------------------------- /test/unittests/pipelines/anatomical/freesurfer/atlas/test_t1_freesurfer_atlas_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/anatomical/freesurfer/atlas/test_t1_freesurfer_atlas_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/anatomical/freesurfer/longitudinal/correction/test_t1_freesurfer_longitudinal_correction_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/anatomical/freesurfer/longitudinal/correction/test_t1_freesurfer_longitudinal_correction_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/anatomical/freesurfer/longitudinal/template/test_t1_freesurfer_longitudinal_template_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/anatomical/freesurfer/longitudinal/template/test_t1_freesurfer_longitudinal_template_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/anatomical/freesurfer/t1/test_t1_freesurfer_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/anatomical/freesurfer/t1/test_t1_freesurfer_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/anatomical/freesurfer/t1/test_t1_freesurfer_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/anatomical/freesurfer/t1/test_t1_freesurfer_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/anatomical/freesurfer/test_freesurfer_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/anatomical/freesurfer/test_freesurfer_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/dwi/connectome/test_dwi_connectome_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/dwi/connectome/test_dwi_connectome_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/dwi/dti/test_dwi_dti_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/dwi/dti/test_dwi_dti_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/dwi/preprocessing/test_common_preprocessing_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/dwi/preprocessing/test_common_preprocessing_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/dwi/preprocessing/test_dwi_preprocessing_using_fmap_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/dwi/preprocessing/test_dwi_preprocessing_using_fmap_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/dwi/preprocessing/test_dwi_preprocessing_using_t1_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/dwi/preprocessing/test_dwi_preprocessing_using_t1_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/dwi/preprocessing/test_fmap_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/dwi/preprocessing/test_fmap_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/dwi/preprocessing/test_t1_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/dwi/preprocessing/test_t1_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/dwi/test_common_dwi_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/dwi/test_common_dwi_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/dwi/test_connectome_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/dwi/test_connectome_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/pet/test_pet_linear_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/pet/test_pet_linear_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/pet/test_pet_linear_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/pet/test_pet_linear_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/pet/test_pet_volume_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/pet/test_pet_volume_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/pet/test_pet_volume_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/pet/test_pet_volume_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/statistics_surface/data/subjects.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/statistics_surface/data/subjects.tsv -------------------------------------------------------------------------------- /test/unittests/pipelines/statistics_surface/test_inputs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/statistics_surface/test_inputs.py -------------------------------------------------------------------------------- /test/unittests/pipelines/statistics_surface/test_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/statistics_surface/test_model.py -------------------------------------------------------------------------------- /test/unittests/pipelines/statistics_volume/test_statistics_volume_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/statistics_volume/test_statistics_volume_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/t1_linear/test_anat_linear_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/t1_linear/test_anat_linear_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/t1_linear/test_anat_linear_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/t1_linear/test_anat_linear_utils.py -------------------------------------------------------------------------------- /test/unittests/pipelines/t1_volume_create_dartel/test_t1_volume_create_dartel_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/t1_volume_create_dartel/test_t1_volume_create_dartel_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/t1_volume_dartel2mni/test_t1_volume_dartel2mni_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/t1_volume_dartel2mni/test_t1_volume_dartel2mni_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/t1_volume_parcellation/test_t1_volume_parcellation_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/t1_volume_parcellation/test_t1_volume_parcellation_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/t1_volume_register_dartel/test_t1_volume_register_dartel_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/t1_volume_register_dartel/test_t1_volume_register_dartel_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/t1_volume_tissue_segmentation/test_t1_volume_tissue_segmentation_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/t1_volume_tissue_segmentation/test_t1_volume_tissue_segmentation_pipeline.py -------------------------------------------------------------------------------- /test/unittests/pipelines/test_nipype_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pipelines/test_nipype_engine.py -------------------------------------------------------------------------------- /test/unittests/pydra/t1_volume/dartel2mni/test_tasks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pydra/t1_volume/dartel2mni/test_tasks.py -------------------------------------------------------------------------------- /test/unittests/pydra/test_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pydra/test_engine.py -------------------------------------------------------------------------------- /test/unittests/pydra/test_interfaces.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pydra/test_interfaces.py -------------------------------------------------------------------------------- /test/unittests/pydra/test_query.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pydra/test_query.py -------------------------------------------------------------------------------- /test/unittests/pydra/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/pydra/test_utils.py -------------------------------------------------------------------------------- /test/unittests/test_testing_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/test_testing_tools.py -------------------------------------------------------------------------------- /test/unittests/utils/test_atlas.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_atlas.py -------------------------------------------------------------------------------- /test/unittests/utils/test_check_dependency.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_check_dependency.py -------------------------------------------------------------------------------- /test/unittests/utils/test_filemanip.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_filemanip.py -------------------------------------------------------------------------------- /test/unittests/utils/test_group.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_group.py -------------------------------------------------------------------------------- /test/unittests/utils/test_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_image.py -------------------------------------------------------------------------------- /test/unittests/utils/test_input_files.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_input_files.py -------------------------------------------------------------------------------- /test/unittests/utils/test_longitudinal.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_longitudinal.py -------------------------------------------------------------------------------- /test/unittests/utils/test_nipype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_nipype.py -------------------------------------------------------------------------------- /test/unittests/utils/test_participant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_participant.py -------------------------------------------------------------------------------- /test/unittests/utils/test_pet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_pet.py -------------------------------------------------------------------------------- /test/unittests/utils/test_spm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_spm.py -------------------------------------------------------------------------------- /test/unittests/utils/test_stream.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_stream.py -------------------------------------------------------------------------------- /test/unittests/utils/test_testing_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_testing_utils.py -------------------------------------------------------------------------------- /test/unittests/utils/test_utils_inputs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_utils_inputs.py -------------------------------------------------------------------------------- /test/unittests/utils/test_ux.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aramis-lab/clinica/HEAD/test/unittests/utils/test_ux.py --------------------------------------------------------------------------------