├── .circleci ├── artifact_path ├── config.yml ├── ds005_fasttrack_outputs.txt ├── ds005_outputs.txt ├── ds005_partial_fasttrack_outputs.txt ├── ds005_partial_outputs.txt ├── ds054_fasttrack_outputs.txt ├── ds054_outputs.txt ├── ds210_fasttrack_outputs.txt ├── ds210_outputs.txt └── legacy.yml ├── .codespellrc ├── .dockerignore ├── .git-blame-ignore-revs ├── .git_archival.txt ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ ├── documentation.md │ └── feature_request.yml ├── config.yml ├── dependabot.yml ├── stale.yml └── workflows │ ├── docker.yml │ ├── pixi-lock.yml │ └── test.yml ├── .gitignore ├── .gitmodules ├── .mailmap ├── .maint ├── CONTRIBUTORS.md ├── FORMER.md ├── MAINTAINERS.md ├── PIs.md ├── update_authors.py ├── update_changes.sh └── update_ignore_revs.sh ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .versions.json ├── .vscode ├── launch.json └── settings.json ├── .zenodo.json ├── CHANGES.rst ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── Dockerfile.base ├── Dockerfile_devel ├── GOVERNANCE.md ├── LICENSE ├── Makefile ├── NOTICE ├── README.rst ├── REFERENCES.md ├── docker └── files │ └── freesurfer7.3.2-exclude.txt ├── docs ├── .gitignore ├── Makefile ├── _static │ ├── EPIT1Normalization.svg │ ├── OHBM2017-poster.png │ ├── OHBM2017-poster_thumb.png │ ├── OHBM2018-poster.png │ ├── OHBM2018-poster_thumb.png │ ├── SampleReport │ │ ├── figures │ │ │ ├── sub-10_desc-reconall_T1w.svg │ │ │ ├── sub-10_dseg.svg │ │ │ ├── sub-10_space-MNI152NLin2009cAsym_T1w.svg │ │ │ ├── sub-10_task-mixedgamblestask_run-1_desc-bbregister_bold.svg │ │ │ ├── sub-10_task-mixedgamblestask_run-1_desc-carpetplot_bold.svg │ │ │ ├── sub-10_task-mixedgamblestask_run-1_desc-compcorvar_bold.svg │ │ │ ├── sub-10_task-mixedgamblestask_run-1_desc-confoundcorr_bold.svg │ │ │ └── sub-10_task-mixedgamblestask_run-1_desc-rois_bold.svg │ │ └── sample_report.html │ ├── T1MNINormalization.svg │ ├── aroma.svg │ ├── fmriprep-21.0.0.svg │ ├── fmriprep-workflow-all.png │ ├── fmriprep_benchmark.svg │ ├── reconall.svg │ ├── sbatch.slurm │ ├── segmentation.svg │ ├── sub-01_dseg.svg │ ├── sub-01_task-balloonanalogrisktask_run-1_desc-rois_bold.svg │ ├── sub-01_task-mixedgamblestask_run-01_confounds_correlation.svg │ ├── sub-01_task-rest_compcor.svg │ ├── sub-405_ses-01_task-rest_run-01_desc-carpetplot_bold.svg │ ├── theme_overrides.css │ └── unwarping.svg ├── api.rst ├── benchmarks.rst ├── changes.rst ├── conf.py ├── faq.rst ├── index.rst ├── installation.rst ├── license.rst ├── links.rst ├── outputs.rst ├── pull_request_template.md ├── requirements.txt ├── spaces.rst ├── sphinxext │ └── github_link.py ├── usage.rst └── workflows.rst ├── fmriprep ├── __init__.py ├── __main__.py ├── _warnings.py ├── cli │ ├── __init__.py │ ├── parser.py │ ├── run.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_parser.py │ │ └── test_version.py │ ├── version.py │ └── workflow.py ├── config.py ├── conftest.py ├── data │ ├── NOTICE │ ├── __init__.py │ ├── boilerplate.bib │ ├── flirtsch │ │ └── bbr.sch │ ├── fmap_spec.json │ ├── io_spec.json │ ├── reports-spec-anat.yml │ ├── reports-spec-func.yml │ ├── reports-spec.yml │ └── tests │ │ ├── config.toml │ │ ├── crash_files │ │ └── crash-20170905-182839-root-dvars-b78e9ea8-e295-48a1-af71-2d36afd9cebf.txt │ │ ├── ds000005 │ │ ├── CHANGES │ │ ├── README │ │ ├── dataset_description.json │ │ ├── participants.tsv │ │ ├── sub-01 │ │ │ ├── anat │ │ │ │ ├── sub-01_T1w.nii.gz │ │ │ │ └── sub-01_inplaneT2.nii.gz │ │ │ └── func │ │ │ │ ├── sub-01_task-mixedgamblestask_run-01_bold.nii.gz │ │ │ │ ├── sub-01_task-mixedgamblestask_run-01_events.tsv │ │ │ │ ├── sub-01_task-mixedgamblestask_run-02_bold.nii.gz │ │ │ │ ├── sub-01_task-mixedgamblestask_run-02_events.tsv │ │ │ │ ├── sub-01_task-mixedgamblestask_run-03_bold.nii.gz │ │ │ │ └── sub-01_task-mixedgamblestask_run-03_events.tsv │ │ └── task-mixedgamblestask_bold.json │ │ ├── logs │ │ └── CITATION.html │ │ └── work │ │ └── reportlets │ │ └── fmriprep │ │ ├── sub-001 │ │ └── figures │ │ │ ├── sub-001_acq-undistorted_desc-conform_T1w.html │ │ │ ├── sub-001_acq-undistorted_desc-reconall_T1w.svg │ │ │ ├── sub-001_acq-undistorted_dseg.svg │ │ │ ├── sub-001_acq-undistorted_space-MNI152NLin2009cAsym_T1w.svg │ │ │ ├── sub-001_desc-about_T1w.html │ │ │ ├── sub-001_desc-conform_T1w.html │ │ │ ├── sub-001_desc-preproc_dseg.svg │ │ │ ├── sub-001_desc-reconall_T1w.svg │ │ │ ├── sub-001_desc-summary_T1w.html │ │ │ ├── sub-001_dseg.svg │ │ │ ├── sub-001_ses-001_task-qct_dir-LR_part-mag_desc-bbregister_bold.svg │ │ │ ├── sub-001_ses-001_task-qct_dir-LR_part-mag_desc-carpetplot_bold.svg │ │ │ ├── sub-001_ses-001_task-qct_dir-LR_part-mag_desc-compcorvar_bold.svg │ │ │ ├── sub-001_ses-001_task-qct_dir-LR_part-mag_desc-confoundcorr_bold.svg │ │ │ ├── sub-001_ses-001_task-qct_dir-LR_part-mag_desc-rois_bold.svg │ │ │ ├── sub-001_ses-001_task-qct_dir-LR_part-mag_desc-summary_bold.html │ │ │ ├── sub-001_ses-001_task-qct_dir-LR_part-mag_desc-t2scomp_bold.svg │ │ │ ├── sub-001_ses-001_task-qct_dir-LR_part-mag_desc-t2starhist_bold.svg │ │ │ ├── sub-001_ses-001_task-qct_dir-LR_part-mag_desc-validation_bold.html │ │ │ ├── sub-001_ses-003_task-qct_dir-LR_part-mag_desc-bbregister_bold.svg │ │ │ ├── sub-001_ses-003_task-qct_dir-LR_part-mag_desc-carpetplot_bold.svg │ │ │ ├── sub-001_ses-003_task-qct_dir-LR_part-mag_desc-compcorvar_bold.svg │ │ │ ├── sub-001_ses-003_task-qct_dir-LR_part-mag_desc-confoundcorr_bold.svg │ │ │ ├── sub-001_ses-003_task-qct_dir-LR_part-mag_desc-rois_bold.svg │ │ │ ├── sub-001_ses-003_task-qct_dir-LR_part-mag_desc-summary_bold.html │ │ │ ├── sub-001_ses-003_task-qct_dir-LR_part-mag_desc-t2scomp_bold.svg │ │ │ ├── sub-001_ses-003_task-qct_dir-LR_part-mag_desc-t2starhist_bold.svg │ │ │ ├── sub-001_ses-003_task-qct_dir-LR_part-mag_desc-validation_bold.html │ │ │ ├── sub-001_ses-004_task-qct_dir-RL_part-mag_desc-bbregister_bold.svg │ │ │ ├── sub-001_ses-004_task-qct_dir-RL_part-mag_desc-carpetplot_bold.svg │ │ │ ├── sub-001_ses-004_task-qct_dir-RL_part-mag_desc-compcorvar_bold.svg │ │ │ ├── sub-001_ses-004_task-qct_dir-RL_part-mag_desc-confoundcorr_bold.svg │ │ │ ├── sub-001_ses-004_task-qct_dir-RL_part-mag_desc-rois_bold.svg │ │ │ ├── sub-001_ses-004_task-qct_dir-RL_part-mag_desc-summary_bold.html │ │ │ ├── sub-001_ses-004_task-qct_dir-RL_part-mag_desc-t2scomp_bold.svg │ │ │ ├── sub-001_ses-004_task-qct_dir-RL_part-mag_desc-t2starhist_bold.svg │ │ │ ├── sub-001_ses-004_task-qct_dir-RL_part-mag_desc-validation_bold.html │ │ │ ├── sub-001_ses-005_task-qct_dir-PA_part-mag_desc-bbregister_bold.svg │ │ │ ├── sub-001_ses-005_task-qct_dir-PA_part-mag_desc-carpetplot_bold.svg │ │ │ ├── sub-001_ses-005_task-qct_dir-PA_part-mag_desc-compcorvar_bold.svg │ │ │ ├── sub-001_ses-005_task-qct_dir-PA_part-mag_desc-confoundcorr_bold.svg │ │ │ ├── sub-001_ses-005_task-qct_dir-PA_part-mag_desc-rois_bold.svg │ │ │ ├── sub-001_ses-005_task-qct_dir-PA_part-mag_desc-summary_bold.html │ │ │ ├── sub-001_ses-005_task-qct_dir-PA_part-mag_desc-t2scomp_bold.svg │ │ │ ├── sub-001_ses-005_task-qct_dir-PA_part-mag_desc-t2starhist_bold.svg │ │ │ ├── sub-001_ses-005_task-qct_dir-PA_part-mag_desc-validation_bold.html │ │ │ ├── sub-001_space-MNI152NLin2009cAsym_T1w.svg │ │ │ └── sub-001_space-MNI152NLin2009cAsym_desc-preproc_T1w.svg │ │ └── sub-01 │ │ ├── anat │ │ ├── sub-01_T1w_conform.html │ │ ├── sub-01_T1w_reconall.html │ │ ├── sub-01_T1w_summary.html │ │ ├── sub-01_T1w_t1_2_mni.svg │ │ ├── sub-01_T1w_t1_seg.html │ │ └── sub-01_T1w_t1_skull_strip.html │ │ └── func │ │ ├── sub-01_task-mixedgamblestask_run-01_bold_acompcor.html │ │ ├── sub-01_task-mixedgamblestask_run-01_bold_bbr.svg │ │ ├── sub-01_task-mixedgamblestask_run-01_bold_bold_mask.html │ │ ├── sub-01_task-mixedgamblestask_run-01_bold_ica_aroma.svg │ │ ├── sub-01_task-mixedgamblestask_run-01_bold_tcompcor.html │ │ ├── sub-01_task-mixedgamblestask_run-01_bold_validation.html │ │ ├── sub-01_task-mixedgamblestask_run-02_bold_acompcor.html │ │ ├── sub-01_task-mixedgamblestask_run-02_bold_bbr.svg │ │ ├── sub-01_task-mixedgamblestask_run-02_bold_bold_mask.html │ │ ├── sub-01_task-mixedgamblestask_run-02_bold_ica_aroma.svg │ │ ├── sub-01_task-mixedgamblestask_run-02_bold_tcompcor.html │ │ └── sub-01_task-mixedgamblestask_run-02_bold_validation.html ├── interfaces │ ├── __init__.py │ ├── bids.py │ ├── confounds.py │ ├── conftest.py │ ├── gifti.py │ ├── maths.py │ ├── multiecho.py │ ├── nitransforms.py │ ├── patches.py │ ├── reports.py │ ├── resampling.py │ ├── tests │ │ ├── __init__.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── acompcor_renamed.tsv │ │ │ ├── acompcor_truncated.tsv │ │ │ ├── bold.nii.gz │ │ │ ├── component_metadata_filtered.tsv │ │ │ ├── component_metadata_renamed.tsv │ │ │ ├── component_metadata_truncated.tsv │ │ │ ├── lh.bold.func.gii │ │ │ ├── lh.midthickness.surf.gii │ │ │ ├── lh.pial.surf.gii │ │ │ ├── lh.roi.shape.gii │ │ │ ├── lh.white.surf.gii │ │ │ ├── mri_coreg-c3d-invert.txt │ │ │ ├── mri_coreg-c3d.txt │ │ │ ├── mri_coreg-lta_convert-invert.txt │ │ │ ├── mri_coreg-lta_convert.mat │ │ │ ├── mri_coreg-lta_convert.txt │ │ │ ├── mri_coreg.lta │ │ │ ├── sub-01_run-01_echo-1_bold.nii.gz │ │ │ ├── sub-01_run-01_echo-2_bold.nii.gz │ │ │ ├── sub-01_run-01_echo-3_bold.nii.gz │ │ │ ├── sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.nii.gz │ │ │ ├── sub-01_task-mixedgamblestask_run-01_desc-motion_timeseries.tsv │ │ │ ├── sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt │ │ │ ├── sub-pixar008_desc-preproc_T1w.nii.gz │ │ │ └── sub-pixar008_task-pixar_desc-coreg_boldref.nii.gz │ │ ├── test_bids.py │ │ ├── test_confounds.py │ │ ├── test_maths.py │ │ ├── test_nitransforms.py │ │ └── test_reports.py │ └── workbench.py ├── reports │ ├── __init__.py │ ├── core.py │ └── tests │ │ ├── __init__.py │ │ └── test_reports.py ├── tests │ 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