├── .github ├── CITATION.cff ├── CONTRIBUTING.md └── workflows │ ├── docbuild.yml │ ├── docker_pyafq.yml │ ├── docker_pyafq_cuda12.yml │ ├── nightly_anisotropic_test.yml │ ├── nightly_basic_test.yml │ ├── nightly_custom_test.yml │ ├── nightly_pft_test.yml │ ├── nightly_reco80_test.yml │ ├── nightly_reco_test.yml │ ├── nightly_test.yml │ ├── publish-to-test-pypi.yml │ └── test.yml ├── .gitignore ├── .mailmap ├── .maintenance ├── update_changes.sh └── update_zenodo.py ├── .pep8speaks.yml ├── .zenodo.json ├── AFQ ├── __init__.py ├── _fixes.py ├── afq_bids_entities.json ├── api │ ├── __init__.py │ ├── bundle_dict.py │ ├── group.py │ ├── participant.py │ └── utils.py ├── data │ ├── __init__.py │ ├── fetch.py │ └── utils.py ├── definitions │ ├── __init__.py │ ├── image.py │ ├── mapping.py │ └── utils.py ├── models │ ├── QBallTP.py │ ├── __init__.py │ ├── csd.py │ ├── dki.py │ ├── dti.py │ └── fwdti.py ├── recognition │ ├── __init__.py │ ├── cleaning.py │ ├── criteria.py │ ├── curvature.py │ ├── preprocess.py │ ├── recognize.py │ ├── roi.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_recognition.py │ │ ├── test_rois.py │ │ └── test_utils.py │ └── utils.py ├── registration.py ├── tasks │ ├── __init__.py │ ├── data.py │ ├── decorators.py │ ├── mapping.py │ ├── segmentation.py │ ├── tractography.py │ ├── utils.py │ └── viz.py ├── tests │ ├── __init__.py │ ├── data │ │ ├── MoriGroups_Test.mat │ │ ├── WholeBrainFG_test.mat │ │ └── mocks3 │ │ │ └── ds000102-mimic │ │ │ ├── .datalad │ │ │ ├── .gitattributes │ │ │ └── config │ │ │ ├── .gitattributes │ │ │ ├── CHANGES │ │ │ ├── README │ │ │ ├── T1w.json │ │ │ ├── annex-uuid │ │ │ ├── dataset_description.json │ │ │ ├── derivatives │ │ │ └── mriqc │ │ │ │ ├── aMRIQC.csv │ │ │ │ ├── anatomical_group.pdf │ │ │ │ ├── anatomical_sub-01.pdf │ │ │ │ ├── anatomical_sub-02.pdf │ │ │ │ ├── anatomical_sub-03.pdf │ │ │ │ ├── anatomical_sub-04.pdf │ │ │ │ ├── anatomical_sub-05.pdf │ │ │ │ ├── anatomical_sub-06.pdf │ │ │ │ ├── anatomical_sub-07.pdf │ │ │ │ ├── anatomical_sub-08.pdf │ │ │ │ ├── anatomical_sub-09.pdf │ │ │ │ ├── anatomical_sub-10.pdf │ │ │ │ ├── anatomical_sub-11.pdf │ │ │ │ ├── anatomical_sub-12.pdf │ │ │ │ ├── anatomical_sub-13.pdf │ │ │ │ ├── anatomical_sub-14.pdf │ │ │ │ ├── anatomical_sub-15.pdf │ │ │ │ ├── anatomical_sub-16.pdf │ │ │ │ ├── anatomical_sub-17.pdf │ │ │ │ ├── anatomical_sub-18.pdf │ │ │ │ ├── anatomical_sub-19.pdf │ │ │ │ ├── anatomical_sub-20.pdf │ │ │ │ ├── anatomical_sub-21.pdf │ │ │ │ ├── anatomical_sub-22.pdf │ │ │ │ ├── anatomical_sub-23.pdf │ │ │ │ ├── anatomical_sub-24.pdf │ │ │ │ ├── anatomical_sub-25.pdf │ │ │ │ ├── anatomical_sub-26.pdf │ │ │ │ ├── fMRIQC.csv │ │ │ │ ├── functional_group.pdf │ │ │ │ ├── functional_sub-01.pdf │ │ │ │ ├── functional_sub-02.pdf │ │ │ │ ├── functional_sub-03.pdf │ │ │ │ ├── functional_sub-04.pdf │ │ │ │ ├── functional_sub-05.pdf │ │ │ │ ├── functional_sub-06.pdf │ │ │ │ ├── functional_sub-07.pdf │ │ │ │ ├── functional_sub-08.pdf │ │ │ │ ├── functional_sub-09.pdf │ │ │ │ ├── functional_sub-10.pdf │ │ │ │ ├── functional_sub-11.pdf │ │ │ │ ├── functional_sub-12.pdf │ │ │ │ ├── functional_sub-13.pdf │ │ │ │ ├── functional_sub-14.pdf │ │ │ │ ├── functional_sub-15.pdf │ │ │ │ ├── functional_sub-16.pdf │ │ │ │ ├── functional_sub-17.pdf │ │ │ │ ├── functional_sub-18.pdf │ │ │ │ ├── functional_sub-19.pdf │ │ │ │ ├── functional_sub-20.pdf │ │ │ │ ├── functional_sub-21.pdf │ │ │ │ ├── functional_sub-22.pdf │ │ │ │ ├── functional_sub-23.pdf │ │ │ │ ├── functional_sub-24.pdf │ │ │ │ ├── functional_sub-25.pdf │ │ │ │ └── functional_sub-26.pdf │ │ │ ├── participants.tsv │ │ │ ├── sub-01 │ │ │ ├── anat │ │ │ │ └── sub-01_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-01_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-01_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-01_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-01_task-flanker_run-2_events.tsv │ │ │ ├── sub-02 │ │ │ ├── anat │ │ │ │ └── sub-02_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-02_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-02_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-02_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-02_task-flanker_run-2_events.tsv │ │ │ ├── sub-03 │ │ │ ├── anat │ │ │ │ └── sub-03_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-03_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-03_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-03_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-03_task-flanker_run-2_events.tsv │ │ │ ├── sub-04 │ │ │ ├── anat │ │ │ │ └── sub-04_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-04_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-04_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-04_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-04_task-flanker_run-2_events.tsv │ │ │ ├── sub-05 │ │ │ ├── anat │ │ │ │ └── sub-05_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-05_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-05_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-05_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-05_task-flanker_run-2_events.tsv │ │ │ ├── sub-06 │ │ │ ├── anat │ │ │ │ └── sub-06_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-06_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-06_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-06_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-06_task-flanker_run-2_events.tsv │ │ │ ├── sub-07 │ │ │ ├── anat │ │ │ │ └── sub-07_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-07_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-07_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-07_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-07_task-flanker_run-2_events.tsv │ │ │ ├── sub-08 │ │ │ ├── anat │ │ │ │ └── sub-08_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-08_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-08_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-08_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-08_task-flanker_run-2_events.tsv │ │ │ ├── sub-09 │ │ │ ├── anat │ │ │ │ └── sub-09_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-09_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-09_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-09_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-09_task-flanker_run-2_events.tsv │ │ │ ├── sub-10 │ │ │ ├── anat │ │ │ │ └── sub-10_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-10_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-10_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-10_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-10_task-flanker_run-2_events.tsv │ │ │ ├── sub-11 │ │ │ ├── anat │ │ │ │ └── sub-11_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-11_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-11_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-11_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-11_task-flanker_run-2_events.tsv │ │ │ ├── sub-12 │ │ │ ├── anat │ │ │ │ └── sub-12_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-12_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-12_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-12_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-12_task-flanker_run-2_events.tsv │ │ │ ├── sub-13 │ │ │ ├── anat │ │ │ │ └── sub-13_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-13_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-13_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-13_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-13_task-flanker_run-2_events.tsv │ │ │ ├── sub-14 │ │ │ ├── anat │ │ │ │ └── sub-14_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-14_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-14_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-14_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-14_task-flanker_run-2_events.tsv │ │ │ ├── sub-15 │ │ │ ├── anat │ │ │ │ └── sub-15_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-15_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-15_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-15_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-15_task-flanker_run-2_events.tsv │ │ │ ├── sub-16 │ │ │ ├── anat │ │ │ │ └── sub-16_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-16_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-16_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-16_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-16_task-flanker_run-2_events.tsv │ │ │ ├── sub-17 │ │ │ ├── anat │ │ │ │ └── sub-17_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-17_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-17_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-17_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-17_task-flanker_run-2_events.tsv │ │ │ ├── sub-18 │ │ │ ├── anat │ │ │ │ └── sub-18_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-18_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-18_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-18_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-18_task-flanker_run-2_events.tsv │ │ │ ├── sub-19 │ │ │ ├── anat │ │ │ │ └── sub-19_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-19_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-19_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-19_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-19_task-flanker_run-2_events.tsv │ │ │ ├── sub-20 │ │ │ ├── anat │ │ │ │ └── sub-20_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-20_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-20_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-20_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-20_task-flanker_run-2_events.tsv │ │ │ ├── sub-21 │ │ │ ├── anat │ │ │ │ └── sub-21_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-21_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-21_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-21_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-21_task-flanker_run-2_events.tsv │ │ │ ├── sub-22 │ │ │ ├── anat │ │ │ │ └── sub-22_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-22_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-22_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-22_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-22_task-flanker_run-2_events.tsv │ │ │ ├── sub-23 │ │ │ ├── anat │ │ │ │ └── sub-23_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-23_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-23_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-23_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-23_task-flanker_run-2_events.tsv │ │ │ ├── sub-24 │ │ │ ├── anat │ │ │ │ └── sub-24_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-24_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-24_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-24_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-24_task-flanker_run-2_events.tsv │ │ │ ├── sub-25 │ │ │ ├── anat │ │ │ │ └── sub-25_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-25_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-25_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-25_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-25_task-flanker_run-2_events.tsv │ │ │ ├── sub-26 │ │ │ ├── anat │ │ │ │ └── sub-26_T1w.nii.gz │ │ │ └── func │ │ │ │ ├── sub-26_task-flanker_run-1_bold.nii.gz │ │ │ │ ├── sub-26_task-flanker_run-1_events.tsv │ │ │ │ ├── sub-26_task-flanker_run-2_bold.nii.gz │ │ │ │ └── sub-26_task-flanker_run-2_events.tsv │ │ │ └── task-flanker_bold.json │ ├── test_api.py │ ├── test_bundle_dict.py │ ├── test_csd.py │ ├── test_data.py │ ├── test_definitions.py │ ├── test_dki.py │ ├── test_dti.py │ ├── test_fixes.py │ ├── test_registration.py │ ├── test_tractography.py │ └── test_viz.py ├── tractography │ ├── __init__.py │ ├── gputractography.py │ ├── tractography.py │ └── utils.py ├── utils │ ├── __init__.py │ ├── bin.py │ ├── conversion.py │ ├── docs.py │ ├── models.py │ ├── path.py │ ├── stats.py │ ├── streamlines.py │ ├── testing.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_conversions.py │ │ ├── test_path.py │ │ ├── test_stats.py │ │ ├── test_streamlines.py │ │ └── test_volume.py │ └── volume.py └── viz │ ├── __init__.py │ ├── altair.py │ ├── fury_backend.py │ ├── plot.py │ ├── plotly_backend.py │ └── utils.py ├── CHANGES.rst ├── CITATION ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── bin └── pyAFQ ├── docs ├── Makefile ├── source │ ├── _progressbars.py │ ├── _static │ │ ├── BDE_Banner_revised20160211-01.jpg │ │ ├── custom.css │ │ ├── eScience_Logo_HR.png │ │ ├── escience-logo.png │ │ └── logo.png │ ├── _templates │ │ └── layout.html │ ├── conf.py │ ├── explanations │ │ ├── _static │ │ │ ├── down_left_arrow.png │ │ │ ├── down_right_arrow.png │ │ │ ├── greencheck.png │ │ │ ├── tract_modeling2.png │ │ │ ├── tract_profiling.png │ │ │ ├── tract_recognition.png │ │ │ └── tract_tractography.png │ │ ├── bundle_orientation.rst │ │ ├── index.rst │ │ ├── modeling.rst │ │ ├── profiling.rst │ │ ├── recognition.rst │ │ ├── tractography.rst │ │ └── tractometry_pipeline.rst │ ├── howto │ │ ├── cite.rst │ │ ├── contributing.rst │ │ ├── developing │ │ │ ├── definitions.rst │ │ │ ├── index.rst │ │ │ ├── releasing.rst │ │ │ └── tasks.rst │ │ ├── getting_help.rst │ │ ├── index.rst │ │ ├── installation_guide.rst │ │ └── usage │ │ │ ├── converter.rst │ │ │ ├── data.rst │ │ │ ├── docker.rst │ │ │ ├── image.rst │ │ │ ├── index.rst │ │ │ ├── kwargs.rst │ │ │ ├── methods.rst │ │ │ └── scalars.rst │ ├── index.rst │ ├── reference │ │ ├── bundledict.rst │ │ ├── index.rst │ │ ├── kwargs.rst │ │ ├── mapping.rst │ │ ├── methods.rst │ │ └── viz_backend.rst │ ├── sphinxext │ │ ├── kwargsdocs.py │ │ ├── methodsdocs.py │ │ └── updatedocs.py │ └── tutorials │ │ └── index.rst └── upload-gh-pages.sh ├── examples ├── howto_examples │ ├── README.rst │ ├── add_custom_bundle.py │ ├── baby_afq.py │ ├── cerebellar_peduncles.py │ ├── cloudknot_example.py │ ├── cloudknot_hcp_example.py │ ├── plot_acoustic_radiations.py │ ├── plot_afq_callosal.py │ ├── plot_afq_fwdti.py │ ├── plot_optic_radiations.py │ ├── plot_recobundles.py │ ├── plot_stages_of_tractometry.py │ ├── use_subject_space_rois_from_freesurfer.py │ └── vof_example.py └── tutorial_examples │ ├── README.rst │ ├── plot_001_afq_api.py │ ├── plot_002_bids_layout.py │ └── plot_003_viz.py ├── gpu_docker ├── Dockerfile ├── cuda_build.sh ├── cuda_track_template.def ├── docker-build.sh └── docker-push.sh ├── pyafq_docker ├── Dockerfile ├── docker-build.sh └── docker-push.sh ├── pyproject.toml ├── setup.cfg ├── setup.py └── tox.ini /.github/CITATION.cff: 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