LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
clinica/VERSION
clinica/__init__.py
clinica/cmdline.py
clinica/compat.py
clinica.egg-info/PKG-INFO
clinica.egg-info/SOURCES.txt
clinica.egg-info/dependency_links.txt
clinica.egg-info/entry_points.txt
clinica.egg-info/not-zip-safe
clinica.egg-info/requires.txt
clinica.egg-info/top_level.txt
clinica/engine/__init__.py
clinica/engine/cmdparser.py
clinica/engine/template.py
clinica/iotools/__init__.py
clinica/iotools/abstract_converter.py
clinica/iotools/bids_utils.py
clinica/iotools/converter_utils.py
clinica/iotools/converters/__init__.py
clinica/iotools/converters/cli.py
clinica/iotools/converters/cli_param.py
clinica/iotools/converters/adni_to_bids/__init__.py
clinica/iotools/converters/adni_to_bids/adni_to_bids.py
clinica/iotools/converters/adni_to_bids/adni_to_bids_cli.py
clinica/iotools/converters/adni_to_bids/adni_utils.py
clinica/iotools/converters/adni_to_bids/adni_modalities/__init__.py
clinica/iotools/converters/adni_to_bids/adni_modalities/adni_av45_fbb_pet.py
clinica/iotools/converters/adni_to_bids/adni_modalities/adni_dwi.py
clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fdg_pet.py
clinica/iotools/converters/adni_to_bids/adni_modalities/adni_flair.py
clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fmri.py
clinica/iotools/converters/adni_to_bids/adni_modalities/adni_pib_pet.py
clinica/iotools/converters/adni_to_bids/adni_modalities/adni_t1.py
clinica/iotools/converters/adni_to_bids/adni_modalities/adni_tau_pet.py
clinica/iotools/converters/aibl_to_bids/__init__.py
clinica/iotools/converters/aibl_to_bids/aibl_to_bids.py
clinica/iotools/converters/aibl_to_bids/aibl_to_bids_cli.py
clinica/iotools/converters/aibl_to_bids/aibl_utils.py
clinica/iotools/converters/clinical_data_bids_correspondence/clinical_data_bids_correspondence_participant.tsv
clinica/iotools/converters/clinical_data_bids_correspondence/clinical_data_bids_correspondence_scans.tsv
clinica/iotools/converters/clinical_data_bids_correspondence/clinical_data_bids_correspondence_sessions.tsv
clinica/iotools/converters/nifd_to_bids/__init__.py
clinica/iotools/converters/nifd_to_bids/nifd_to_bids.py
clinica/iotools/converters/nifd_to_bids/nifd_to_bids_cli.py
clinica/iotools/converters/nifd_to_bids/nifd_utils.py
clinica/iotools/converters/oasis3_to_bids/__init__.py
clinica/iotools/converters/oasis3_to_bids/oasis3_to_bids.py
clinica/iotools/converters/oasis3_to_bids/oasis3_to_bids_cli.py
clinica/iotools/converters/oasis3_to_bids/oasis3_utils.py
clinica/iotools/converters/oasis_to_bids/__init__.py
clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py
clinica/iotools/converters/oasis_to_bids/oasis_to_bids_cli.py
clinica/iotools/data/clinical_specifications_adni_participant.tsv
clinica/iotools/data/clinical_specifications_adni_scans.tsv
clinica/iotools/data/clinical_specifications_adni_sessions.tsv
clinica/iotools/data/clinical_specifications_participant.tsv
clinica/iotools/data/clinical_specifications_scans.tsv
clinica/iotools/data/clinical_specifications_sessions.tsv
clinica/iotools/data/modality_equiv.tsv
clinica/iotools/utils/__init__.py
clinica/iotools/utils/cli.py
clinica/iotools/utils/data_handling.py
clinica/iotools/utils/pipeline_handling.py
clinica/lib/__init__.py
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clinica/lib/nipype/interfaces/mrtrix3/reconst.py
clinica/lib/nipype/interfaces/mrtrix3/tracking.py
clinica/lib/nipype/interfaces/mrtrix3/utils.py
clinica/pipelines/__init__.py
clinica/pipelines/cli.py
clinica/pipelines/engine.py
clinica/pipelines/cli_param/__init__.py
clinica/pipelines/cli_param/argument.py
clinica/pipelines/cli_param/option.py
clinica/pipelines/cli_param/option_group.py
clinica/pipelines/deeplearning_prepare_data/__init__.py
clinica/pipelines/deeplearning_prepare_data/deeplearning_prepare_data_cli.py
clinica/pipelines/deeplearning_prepare_data/deeplearning_prepare_data_pipeline.py
clinica/pipelines/deeplearning_prepare_data/deeplearning_prepare_data_utils.py
clinica/pipelines/deeplearning_prepare_data/info.json
clinica/pipelines/dwi_connectome/__init__.py
clinica/pipelines/dwi_connectome/dwi_connectome_cli.py
clinica/pipelines/dwi_connectome/dwi_connectome_pipeline.py
clinica/pipelines/dwi_connectome/dwi_connectome_utils.py
clinica/pipelines/dwi_connectome/info.json
clinica/pipelines/dwi_dti/__init__.py
clinica/pipelines/dwi_dti/dwi_dti_cli.py
clinica/pipelines/dwi_dti/dwi_dti_pipeline.py
clinica/pipelines/dwi_dti/dwi_dti_utils.py
clinica/pipelines/dwi_dti/info.json
clinica/pipelines/dwi_preprocessing_using_phasediff_fieldmap/__init__.py
clinica/pipelines/dwi_preprocessing_using_phasediff_fieldmap/dwi_preprocessing_using_phasediff_fieldmap_cli.py
clinica/pipelines/dwi_preprocessing_using_phasediff_fieldmap/dwi_preprocessing_using_phasediff_fieldmap_pipeline.py
clinica/pipelines/dwi_preprocessing_using_phasediff_fieldmap/dwi_preprocessing_using_phasediff_fieldmap_utils.py
clinica/pipelines/dwi_preprocessing_using_phasediff_fieldmap/dwi_preprocessing_using_phasediff_fieldmap_workflows.py
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clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_cli.py
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clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_workflows.py
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clinica/pipelines/machine_learning/__init__.py
clinica/pipelines/machine_learning/algorithm.py
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clinica/pipelines/machine_learning/classification_cli.py
clinica/pipelines/machine_learning/input.py
clinica/pipelines/machine_learning/ml_utils.py
clinica/pipelines/machine_learning/ml_workflows.py
clinica/pipelines/machine_learning/region_based_io.py
clinica/pipelines/machine_learning/tsv_based_io.py
clinica/pipelines/machine_learning/validation.py
clinica/pipelines/machine_learning/vertex_based_io.py
clinica/pipelines/machine_learning/voxel_based_io.py
clinica/pipelines/machine_learning_spatial_svm/__init__.py
clinica/pipelines/machine_learning_spatial_svm/info.json
clinica/pipelines/machine_learning_spatial_svm/spatial_svm_cli.py
clinica/pipelines/machine_learning_spatial_svm/spatial_svm_pipeline.py
clinica/pipelines/machine_learning_spatial_svm/spatial_svm_utils.py
clinica/pipelines/pet_linear/__init__.py
clinica/pipelines/pet_linear/info.json
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clinica/pipelines/pet_surface/applyInverseDeformationField.m
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clinica/pipelines/pet_surface/pet_surface_cli.py
clinica/pipelines/pet_surface/pet_surface_longitudinal_cli.py
clinica/pipelines/pet_surface/pet_surface_pipeline.py
clinica/pipelines/pet_surface/pet_surface_utils.py
clinica/pipelines/pet_volume/__init__.py
clinica/pipelines/pet_volume/info.json
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clinica/pipelines/pet_volume/pet_volume_pipeline.py
clinica/pipelines/pet_volume/pet_volume_utils.py
clinica/pipelines/statistics_surface/__init__.py
clinica/pipelines/statistics_surface/info.json
clinica/pipelines/statistics_surface/statistics_surface_cli.py
clinica/pipelines/statistics_surface/statistics_surface_pipeline.py
clinica/pipelines/statistics_surface/statistics_surface_utils.py
clinica/pipelines/statistics_volume/__init__.py
clinica/pipelines/statistics_volume/info.json
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clinica/pipelines/statistics_volume/statistics_volume_pipeline.py
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clinica/pipelines/statistics_volume/template_model_estimation.m
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clinica/pipelines/statistics_volume_correction/info.json
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clinica/pipelines/statistics_volume_correction/statistics_volume_correction_pipeline.py
clinica/pipelines/statistics_volume_correction/statistics_volume_correction_utils.py
clinica/pipelines/t1_freesurfer/__init__.py
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clinica/pipelines/t1_freesurfer/t1_freesurfer_visualizer.py
clinica/pipelines/t1_freesurfer_longitudinal/__init__.py
clinica/pipelines/t1_freesurfer_longitudinal/info.json
clinica/pipelines/t1_freesurfer_longitudinal/longitudinal_utils.py
clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_longitudinal_cli.py
clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_longitudinal_correction_cli.py
clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_longitudinal_correction_pipeline.py
clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_longitudinal_correction_utils.py
clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_template_cli.py
clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_template_pipeline.py
clinica/pipelines/t1_freesurfer_longitudinal/t1_freesurfer_template_utils.py
clinica/pipelines/t1_linear/__init__.py
clinica/pipelines/t1_linear/info.json
clinica/pipelines/t1_linear/t1_linear_cli.py
clinica/pipelines/t1_linear/t1_linear_pipeline.py
clinica/pipelines/t1_linear/t1_linear_utils.py
clinica/pipelines/t1_linear/t1_linear_visualizer.py
clinica/pipelines/t1_volume/__init__.py
clinica/pipelines/t1_volume/info.json
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clinica/pipelines/t1_volume_create_dartel/info.json
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clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_pipeline.py
clinica/pipelines/t1_volume_dartel2mni/__init__.py
clinica/pipelines/t1_volume_dartel2mni/info.json
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clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_pipeline.py
clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_utils.py
clinica/pipelines/t1_volume_existing_template/__init__.py
clinica/pipelines/t1_volume_existing_template/info.json
clinica/pipelines/t1_volume_existing_template/t1_volume_existing_template_cli.py
clinica/pipelines/t1_volume_parcellation/__init__.py
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clinica/pipelines/t1_volume_tissue_segmentation/__init__.py
clinica/pipelines/t1_volume_tissue_segmentation/info.json
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clinica/utils/atlas.py
clinica/utils/check_dependency.py
clinica/utils/dwi.py
clinica/utils/epi.py
clinica/utils/exceptions.py
clinica/utils/filemanip.py
clinica/utils/fmap.py
clinica/utils/freesurfer.py
clinica/utils/group.py
clinica/utils/input_files.py
clinica/utils/inputs.py
clinica/utils/longitudinal.py
clinica/utils/mri_registration.py
clinica/utils/nipype.py
clinica/utils/participant.py
clinica/utils/pet.py
clinica/utils/spm.py
clinica/utils/statistics.py
clinica/utils/stream.py
clinica/utils/ux.py
clinica/workflows/__init__.py
clinica/workflows/dwi_preprocessing.py
test/__init__.py
test/conftest.py
test/nonregression/__init__.py
test/nonregression/testing_tools.py