├── .circleci ├── artifact_path ├── config.yml └── version.py ├── .codecov.yml ├── .coveragerc ├── .docker └── files │ ├── neurodebian.gpg │ └── nipype.cfg ├── .dockerignore ├── .git-blame-ignore-revs ├── .git_archival.txt ├── .gitattributes ├── .github ├── dependabot.yml └── workflows │ ├── build-test-publish.yml │ ├── docs-build-update.yml │ └── validate.yml ├── .gitignore ├── .mailmap ├── .maint ├── CONTRIBUTORS.md ├── FORMER.md ├── MAINTAINERS.md ├── PIs.md ├── ROADMAP.md └── update_authors.py ├── .pep8speaks.yml ├── .pre-commit-config.yaml ├── .zenodo.json ├── CHANGES.rst ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── Makefile ├── README.rst ├── docs ├── Makefile ├── _static │ ├── config-example.toml │ ├── css │ │ └── version-switch.css │ ├── js │ │ └── version-switch.js │ └── sdcflows-OHBM21-fig1.png ├── _templates │ └── sidebar │ │ └── brand.html ├── api.rst ├── changes.rst ├── cli.rst ├── conf.py ├── examples.rst ├── index.rst ├── installation.rst ├── links.rst ├── methods.rst ├── notebooks │ ├── SDC - Theory and physics.ipynb │ └── fieldmap.nii.gz ├── reference │ └── .gitignore ├── requirements.txt └── tools │ ├── LICENSE.txt │ ├── apigen.py │ └── buildmodref.py ├── env.yml ├── pyproject.toml ├── requirements.txt ├── sdcflows ├── __init__.py ├── _warnings.py ├── cli │ ├── __init__.py │ ├── main.py │ ├── parser.py │ ├── tests │ │ ├── __init__.py │ │ └── test_find_estimators.py │ └── workflow.py ├── config.py ├── conftest.py ├── data │ ├── __init__.py │ ├── affine.json │ ├── flirtsch │ │ ├── b02b0.cnf │ │ ├── b02b0_1.cnf │ │ ├── b02b0_2.cnf │ │ ├── b02b0_4.cnf │ │ └── b02b0_quick.cnf │ ├── fmap-any_registration.json │ ├── fmap-any_registration_testing.json │ ├── fmap_atlas.nii.gz │ ├── fmap_atlas_2_MNI152NLin2009cAsym_affine.mat │ ├── sd_syn.json │ ├── sd_syn_sloppy.json │ └── translation_rigid.json ├── fieldmaps.py ├── interfaces │ ├── __init__.py │ ├── brainmask.py │ ├── bspline.py │ ├── epi.py │ ├── fmap.py │ ├── reportlets.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_bspline.py │ │ ├── test_epi.py │ │ ├── test_fmap.py │ │ ├── test_reportlets.py │ │ └── test_utils.py │ └── utils.py ├── tests │ ├── __init__.py │ ├── data │ │ ├── dsA │ │ │ ├── dataset_description.json │ │ │ └── sub-01 │ │ │ │ ├── anat │ │ │ │ ├── sub-01_FLAIR.nii.gz │ │ │ │ ├── sub-01_T1w.nii.gz │ │ │ │ └── sub-01_T2w.nii.gz │ │ │ │ ├── dwi │ │ │ │ ├── sub-01_dir-AP_dwi.nii.gz │ │ │ │ ├── sub-01_dir-AP_sbref.json │ │ │ │ ├── sub-01_dir-AP_sbref.nii.gz │ │ │ │ ├── sub-01_dir-LR_dwi.nii.gz │ │ │ │ ├── sub-01_dir-LR_sbref.json │ │ │ │ ├── sub-01_dir-LR_sbref.nii.gz │ │ │ │ ├── sub-01_dir-PA_dwi.nii.gz │ │ │ │ ├── sub-01_dir-PA_sbref.json │ │ │ │ ├── sub-01_dir-PA_sbref.nii.gz │ │ │ │ ├── sub-01_dir-RL_dwi.nii.gz │ │ │ │ ├── sub-01_dir-RL_sbref.json │ │ │ │ └── sub-01_dir-RL_sbref.nii.gz │ │ │ │ ├── fmap │ │ │ │ ├── sub-01_acq-single_dir-PA_epi.json │ │ │ │ ├── sub-01_acq-single_dir-PA_epi.nii.gz │ │ │ │ ├── sub-01_dir-AP_epi.json │ │ │ │ ├── sub-01_dir-AP_epi.nii.gz │ │ │ │ ├── sub-01_dir-LR_epi.json │ │ │ │ ├── sub-01_dir-LR_epi.nii.gz │ │ │ │ ├── sub-01_dir-PA_epi.json │ │ │ │ ├── sub-01_dir-PA_epi.nii.gz │ │ │ │ ├── sub-01_dir-RL_epi.json │ │ │ │ ├── sub-01_dir-RL_epi.nii.gz │ │ │ │ ├── sub-01_fieldmap.json │ │ │ │ ├── sub-01_fieldmap.nii.gz │ │ │ │ ├── sub-01_magnitude.nii.gz │ │ │ │ ├── sub-01_magnitude1.nii.gz │ │ │ │ ├── sub-01_magnitude2.nii.gz │ │ │ │ ├── sub-01_phase1.json │ │ │ │ ├── sub-01_phase1.nii.gz │ │ │ │ ├── sub-01_phase2.json │ │ │ │ ├── sub-01_phase2.nii.gz │ │ │ │ ├── sub-01_phasediff.json │ │ │ │ └── sub-01_phasediff.nii.gz │ │ │ │ └── func │ │ │ │ ├── sub-01_task-rest_bold.nii.gz │ │ │ │ └── sub-01_task-rest_sbref.nii.gz │ │ ├── dsB │ │ │ ├── dataset_description.json │ │ │ └── sub-01 │ │ │ │ └── ses-1 │ │ │ │ ├── anat │ │ │ │ ├── sub-01_ses-1_FLAIR.nii.gz │ │ │ │ ├── sub-01_ses-1_T1w.nii.gz │ │ │ │ └── sub-01_ses-1_T2w.nii.gz │ │ │ │ ├── dwi │ │ │ │ ├── sub-01_ses-1_dir-AP_dwi.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-AP_sbref.json │ │ │ │ ├── sub-01_ses-1_dir-AP_sbref.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-LR_dwi.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-LR_sbref.json │ │ │ │ ├── sub-01_ses-1_dir-LR_sbref.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-PA_dwi.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-PA_sbref.json │ │ │ │ ├── sub-01_ses-1_dir-PA_sbref.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-RL_dwi.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-RL_sbref.json │ │ │ │ └── sub-01_ses-1_dir-RL_sbref.nii.gz │ │ │ │ ├── fmap │ │ │ │ ├── sub-01_ses-1_acq-single_dir-PA_epi.json │ │ │ │ ├── sub-01_ses-1_acq-single_dir-PA_epi.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-AP_epi.json │ │ │ │ ├── sub-01_ses-1_dir-AP_epi.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-LR_epi.json │ │ │ │ ├── sub-01_ses-1_dir-LR_epi.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-PA_epi.json │ │ │ │ ├── sub-01_ses-1_dir-PA_epi.nii.gz │ │ │ │ ├── sub-01_ses-1_dir-RL_epi.json │ │ │ │ ├── sub-01_ses-1_dir-RL_epi.nii.gz │ │ │ │ ├── sub-01_ses-1_fieldmap.json │ │ │ │ ├── sub-01_ses-1_fieldmap.nii.gz │ │ │ │ ├── sub-01_ses-1_magnitude.nii.gz │ │ │ │ ├── sub-01_ses-1_magnitude1.nii.gz │ │ │ │ ├── sub-01_ses-1_magnitude2.nii.gz │ │ │ │ ├── sub-01_ses-1_phase1.json │ │ │ │ ├── sub-01_ses-1_phase1.nii.gz │ │ │ │ ├── sub-01_ses-1_phase2.json │ │ │ │ ├── sub-01_ses-1_phase2.nii.gz │ │ │ │ ├── sub-01_ses-1_phasediff.json │ │ │ │ └── sub-01_ses-1_phasediff.nii.gz │ │ │ │ └── func │ │ │ │ ├── sub-01_ses-1_task-rest_bold.nii.gz │ │ │ │ └── sub-01_ses-1_task-rest_sbref.nii.gz │ │ ├── dsC │ │ │ ├── dataset_description.json │ │ │ ├── sub-01 │ │ │ │ ├── anat │ │ │ │ │ ├── sub-01_FLAIR.nii.gz │ │ │ │ │ ├── sub-01_T1w.nii.gz │ │ │ │ │ └── sub-01_T2w.nii.gz │ │ │ │ ├── dwi │ │ │ │ │ ├── sub-01_dir-AP_dwi.nii.gz │ │ │ │ │ ├── sub-01_dir-AP_sbref.json │ │ │ │ │ ├── sub-01_dir-AP_sbref.nii.gz │ │ │ │ │ ├── sub-01_dir-LR_dwi.nii.gz │ │ │ │ │ ├── sub-01_dir-LR_sbref.json │ │ │ │ │ ├── sub-01_dir-LR_sbref.nii.gz │ │ │ │ │ ├── sub-01_dir-PA_dwi.nii.gz │ │ │ │ │ ├── sub-01_dir-PA_sbref.json │ │ │ │ │ ├── sub-01_dir-PA_sbref.nii.gz │ │ │ │ │ ├── sub-01_dir-RL_dwi.nii.gz │ │ │ │ │ ├── sub-01_dir-RL_sbref.json │ │ │ │ │ └── sub-01_dir-RL_sbref.nii.gz │ │ │ │ ├── fmap │ │ │ │ │ ├── sub-01_acq-single_dir-PA_epi.json │ │ │ │ │ ├── sub-01_acq-single_dir-PA_epi.nii.gz │ │ │ │ │ ├── sub-01_dir-AP_epi.json │ │ │ │ │ ├── sub-01_dir-AP_epi.nii.gz │ │ │ │ │ ├── sub-01_dir-LR_epi.json │ │ │ │ │ ├── sub-01_dir-LR_epi.nii.gz │ │ │ │ │ ├── sub-01_dir-PA_epi.json │ │ │ │ │ ├── sub-01_dir-PA_epi.nii.gz │ │ │ │ │ ├── sub-01_dir-RL_epi.json │ │ │ │ │ ├── sub-01_dir-RL_epi.nii.gz │ │ │ │ │ ├── sub-01_fieldmap.json │ │ │ │ │ ├── sub-01_fieldmap.nii.gz │ │ │ │ │ ├── sub-01_magnitude.nii.gz │ │ │ │ │ ├── sub-01_magnitude1.nii.gz │ │ │ │ │ ├── sub-01_magnitude2.nii.gz │ │ │ │ │ ├── sub-01_phase1.json │ │ │ │ │ ├── sub-01_phase1.nii.gz │ │ │ │ │ ├── sub-01_phase2.json │ │ │ │ │ ├── sub-01_phase2.nii.gz │ │ │ │ │ ├── sub-01_phasediff.json │ │ │ │ │ └── sub-01_phasediff.nii.gz │ │ │ │ └── func │ │ │ │ │ ├── sub-01_task-rest_bold.nii.gz │ │ │ │ │ └── sub-01_task-rest_sbref.nii.gz │ │ │ └── task-rest_bold.json │ │ ├── epi.nii.gz │ │ ├── epi2fmap_xfm.txt │ │ ├── field-coeff-tests.nii.gz │ │ ├── fmap2epi_xfm.txt │ │ ├── topup-coeff-fixed.nii.gz │ │ ├── topup-coeff.nii.gz │ │ └── topup-field.nii.gz │ ├── test_fieldmaps.py │ ├── test_transform.py │ └── test_version.py ├── transform.py ├── utils │ ├── __init__.py │ ├── bimap.py │ ├── epimanip.py │ ├── misc.py │ ├── phasemanip.py │ ├── telemetry.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_misc.py │ │ ├── test_phasemanip.py │ │ ├── test_tools.py │ │ └── test_wrangler.py │ ├── tools.py │ └── wrangler.py ├── viz │ ├── __init__.py │ └── utils.py └── workflows │ ├── __init__.py │ ├── ancillary.py │ ├── apply │ ├── __init__.py │ ├── correction.py │ ├── registration.py │ └── tests │ │ ├── __init__.py │ │ ├── test_correction.py │ │ └── test_registration.py │ ├── base.py │ ├── fit │ ├── 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