LICENSE.txt
MANIFEST.in
README.md
setup.cfg
setup.py
clinica/VERSION
clinica/__init__.py
clinica/cmdline.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/grabcaps.py
clinica/iotools/converters/__init__.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_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_t1.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/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.xlsx
clinica/iotools/data/clinical_specifications_adni.xlsx
clinica/iotools/data/modality_equiv.xlsx
clinica/iotools/utils/__init__.py
clinica/iotools/utils/data_handling.py
clinica/iotools/utils/data_handling_cli.py
clinica/iotools/utils/pipeline_handling.py
clinica/lib/__init__.py
clinica/lib/clinicasurfstat/clinicasurfstat.m
clinica/lib/clinicasurfstat/SurfStat/I.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatAvSurf.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatAvVol.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatColLim.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatColormap.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatCoord2Ind.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatDataCursor.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatDataCursorP.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatDataCursorQ.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatDelete.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatEdg.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatF.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatInd2Coord.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatInflate.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatLinMod.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatListDir.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatMaskCut.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatNorm.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatP.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatPCA.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatPeakClus.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatPlot.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatQ.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatROI.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatReadData.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatReadData1.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatReadSurf.m
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clinica/lib/clinicasurfstat/SurfStat/SurfStatReadVol.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatReadVol1.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatResels.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatSmooth.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatStand.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatSurf2Vol.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatT.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatView.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatView1.m
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clinica/lib/clinicasurfstat/SurfStat/SurfStatViewData_backup.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatView_backup.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatViews.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatVol2Surf.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatWriteData.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatWriteSurf.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatWriteSurf1.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatWriteVol.m
clinica/lib/clinicasurfstat/SurfStat/SurfStatWriteVol1.m
clinica/lib/clinicasurfstat/SurfStat/fac2var.m
clinica/lib/clinicasurfstat/SurfStat/gl.m
clinica/lib/clinicasurfstat/SurfStat/icbm_template_2.00mm+orig.HEAD
clinica/lib/clinicasurfstat/SurfStat/icbm_template_2.00mm.hdr
clinica/lib/clinicasurfstat/SurfStat/icbm_template_2.00mm.mnc
clinica/lib/clinicasurfstat/SurfStat/redmod.m
clinica/lib/clinicasurfstat/SurfStat/spectral.m
clinica/lib/clinicasurfstat/SurfStat/stat_threshold.m
clinica/lib/clinicasurfstat/SurfStat/var2fac.m
clinica/lib/clinicasurfstat/SurfStat/@random/char.m
clinica/lib/clinicasurfstat/SurfStat/@random/display.m
clinica/lib/clinicasurfstat/SurfStat/@random/double.m
clinica/lib/clinicasurfstat/SurfStat/@random/image.m
clinica/lib/clinicasurfstat/SurfStat/@random/isempty.m
clinica/lib/clinicasurfstat/SurfStat/@random/minus.m
clinica/lib/clinicasurfstat/SurfStat/@random/mpower.m
clinica/lib/clinicasurfstat/SurfStat/@random/mtimes.m
clinica/lib/clinicasurfstat/SurfStat/@random/plus.m
clinica/lib/clinicasurfstat/SurfStat/@random/random.m
clinica/lib/clinicasurfstat/SurfStat/@random/size.m
clinica/lib/clinicasurfstat/SurfStat/@random/subsref.m
clinica/lib/clinicasurfstat/SurfStat/@term/char.m
clinica/lib/clinicasurfstat/SurfStat/@term/display.m
clinica/lib/clinicasurfstat/SurfStat/@term/double.m
clinica/lib/clinicasurfstat/SurfStat/@term/image.m
clinica/lib/clinicasurfstat/SurfStat/@term/isempty.m
clinica/lib/clinicasurfstat/SurfStat/@term/minus.m
clinica/lib/clinicasurfstat/SurfStat/@term/mpower.m
clinica/lib/clinicasurfstat/SurfStat/@term/mtimes.m
clinica/lib/clinicasurfstat/SurfStat/@term/plus.m
clinica/lib/clinicasurfstat/SurfStat/@term/size.m
clinica/lib/clinicasurfstat/SurfStat/@term/subsref.m
clinica/lib/clinicasurfstat/SurfStat/@term/term.m
clinica/lib/nipype/interfaces/mrtrix/preprocess.py
clinica/lib/nipype/interfaces/mrtrix3/reconst.py
clinica/lib/nipype/interfaces/mrtrix3/tracking.py
clinica/lib/nipype/interfaces/mrtrix3/utils.py
clinica/lib/pycaps/__init__.py
clinica/lib/pycaps/caps_layout.py
clinica/lib/pycaps/config/caps.json
clinica/pipelines/__init__.py
clinica/pipelines/engine.py
clinica/pipelines/space_required_by_pipeline.csv
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/dwi_dti_workflows.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
clinica/pipelines/dwi_preprocessing_using_phasediff_fieldmap/info.json
clinica/pipelines/dwi_preprocessing_using_t1/__init__.py
clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_cli.py
clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_pipeline.py
clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_utils.py
clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_workflows.py
clinica/pipelines/dwi_preprocessing_using_t1/info.json
clinica/pipelines/fmri_preprocessing/__init__.py
clinica/pipelines/fmri_preprocessing/fmri_preprocessing_cli.py
clinica/pipelines/fmri_preprocessing/fmri_preprocessing_pipeline.py
clinica/pipelines/fmri_preprocessing/fmri_preprocessing_utils.py
clinica/pipelines/fmri_preprocessing/info.json
clinica/pipelines/machine_learning/__init__.py
clinica/pipelines/machine_learning/algorithm.py
clinica/pipelines/machine_learning/base.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_surface/__init__.py
clinica/pipelines/pet_surface/info.json
clinica/pipelines/pet_surface/pet_surface_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
clinica/pipelines/pet_volume/pet_volume_cli.py
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/t1_freesurfer_cross_sectional/__init__.py
clinica/pipelines/t1_freesurfer_cross_sectional/info.json
clinica/pipelines/t1_freesurfer_cross_sectional/t1_freesurfer_cross_sectional_cli.py
clinica/pipelines/t1_freesurfer_cross_sectional/t1_freesurfer_cross_sectional_pipeline.py
clinica/pipelines/t1_freesurfer_cross_sectional/t1_freesurfer_cross_sectional_utils.py
clinica/pipelines/t1_freesurfer_cross_sectional/t1_freesurfer_cross_sectional_visualizer.py
clinica/pipelines/t1_volume_create_dartel/__init__.py
clinica/pipelines/t1_volume_create_dartel/info.json
clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_cli.py
clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_pipeline.py
clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_utils.py
clinica/pipelines/t1_volume_dartel2mni/__init__.py
clinica/pipelines/t1_volume_dartel2mni/info.json
clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_cli.py
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_dartel/__init__.py
clinica/pipelines/t1_volume_existing_dartel/info.json
clinica/pipelines/t1_volume_existing_dartel/t1_volume_existing_dartel_cli.py
clinica/pipelines/t1_volume_existing_dartel/t1_volume_existing_dartel_pipeline.py
clinica/pipelines/t1_volume_existing_dartel/t1_volume_existing_dartel_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_existing_template/t1_volume_existing_template_pipeline.py
clinica/pipelines/t1_volume_existing_template/t1_volume_existing_template_utils.py
clinica/pipelines/t1_volume_new_template/__init__.py
clinica/pipelines/t1_volume_new_template/info.json
clinica/pipelines/t1_volume_new_template/t1_volume_new_template_cli.py
clinica/pipelines/t1_volume_new_template/t1_volume_new_template_pipeline.py
clinica/pipelines/t1_volume_parcellation/__init__.py
clinica/pipelines/t1_volume_parcellation/info.json
clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_cli.py
clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_pipeline.py
clinica/pipelines/t1_volume_parcellation/t1_volume_parcellation_utils.py
clinica/pipelines/t1_volume_tissue_segmentation/__init__.py
clinica/pipelines/t1_volume_tissue_segmentation/info.json
clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py
clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_pipeline.py
clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_utils.py
clinica/resources/label_conversion_gtmsegmentation.csv
clinica/resources/atlases/JHUDTI81_FS_LUT.txt
clinica/resources/atlases/JHUDTI81_FS_LUT_newformat.txt
clinica/resources/atlases/JHUDTI81_ROI.tsv
clinica/resources/atlases/JHUTract_FS_LUT.txt
clinica/resources/atlases/JHUTract_FS_LUT_newformat.txt
clinica/resources/atlases/JHUTract_ROI.tsv
clinica/resources/atlases_spm/AAL2.nii
clinica/resources/atlases_spm/AAL2.txt
clinica/resources/atlases_spm/AAL2_ROI.tsv
clinica/resources/atlases_spm/AICHA.nii
clinica/resources/atlases_spm/AICHA.txt
clinica/resources/atlases_spm/AICHA_ROI.tsv
clinica/resources/atlases_spm/Hammers_ROI.tsv
clinica/resources/atlases_spm/LPBA40_ROI.tsv
clinica/resources/atlases_spm/MCALT_ADIR122.nii
clinica/resources/atlases_spm/MCALT_ADIR122_ROI.tsv
clinica/resources/atlases_spm/Neuromorphometrics_ROI.tsv
clinica/resources/atlases_spm/atlas_list.tsv
clinica/resources/atlases_spm/lut_AAL2.txt
clinica/resources/atlases_spm/lut_AAL2_newformat.txt
clinica/resources/atlases_spm/lut_AICHA.txt
clinica/resources/atlases_spm/lut_AICHA_newformat.txt
clinica/resources/atlases_spm/lut_Hammers.txt
clinica/resources/atlases_spm/lut_Hammers_newformat.txt
clinica/resources/atlases_spm/lut_LPBA40.txt
clinica/resources/atlases_spm/lut_LPBA40_newformat.txt
clinica/resources/atlases_spm/lut_MCALT_ADIR122.txt
clinica/resources/atlases_spm/lut_Neuromorphometrics.txt
clinica/resources/atlases_spm/lut_Neuromorphometrics_newformat.txt
clinica/resources/layouts/caps.json
clinica/resources/masks/region-cerebellumPons_eroded-6mm_mask.nii.gz
clinica/resources/masks/region-pons_eroded-6mm_mask.nii.gz
clinica/resources/templates/pipeline_template/README.md.j2
clinica/resources/templates/pipeline_template/__init__.py.j2
clinica/resources/templates/pipeline_template/cli.py.j2
clinica/resources/templates/pipeline_template/info.json.j2
clinica/resources/templates/pipeline_template/pipeline.py.j2
clinica/resources/templates/pipeline_template/utils.py.j2
clinica/resources/templates/pipeline_template/visualizer.py.j2
clinica/utils/__init__.py
clinica/utils/atlas.py
clinica/utils/check_dependency.py
clinica/utils/dwi.py
clinica/utils/epi.py
clinica/utils/exceptions.py
clinica/utils/fmap.py
clinica/utils/freesurfer.py
clinica/utils/fsl.py
clinica/utils/io.py
clinica/utils/mri_registration.py
clinica/utils/mrtrix.py
clinica/utils/statistics.py
clinica/utils/stream.py
clinica/workflows/__init__.py
clinica/workflows/dwi_preprocessing.py
clinica/workflows/dwi_registration.py
test/__init__.py
test/conftest.py
test/test_coding_style.py