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Merge branch 'nipreps:master' into enh/left-right-flip-detection
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‎.circleci/ds005_fasttrack_outputs.txt‎

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sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
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sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
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sub-01/func
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sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
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sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
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sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
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sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json
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sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
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sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
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‎.circleci/ds005_outputs.txt‎

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sub-01/anat/sub-01_label-GM_probseg.nii.gz
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sub-01/anat/sub-01_label-WM_probseg.nii.gz
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sub-01/func
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sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
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sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
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sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
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sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
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‎.circleci/ds005_partial_fasttrack_outputs.txt‎

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sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
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sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
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sub-01/func
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
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‎.circleci/ds005_partial_outputs.txt‎

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sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
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‎.mailmap‎

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Anibal Sólon Heinsfeld <anibalsolon@gmail.com>
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Asier Erramuzpe <asier.erramuzpe@gmail.com>
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Basile Pinsard <basile.pinsard@umontreal.ca>
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Basile Pinsard <basile.pinsard@umontreal.ca> basile <basile.pinsard@gmail.com>
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Basile Pinsard <basile.pinsard@umontreal.ca> <basile.pinsard@gmail.com>
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Basile Pinsard <basile.pinsard@umontreal.ca> <bpinsard@imed.jussieu.fr>
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Blaise Frederick <blaise.frederick@gmail.com>
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Blaise Frederick <blaise.frederick@gmail.com> bbfrederick <blaise.frederick@gmail.com>
@@ -60,6 +60,7 @@ Pablo Velasco <pablo.velasco@nyu.edu>
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Rastko Ciric <rc042010@mymail.pomona.edu>
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Rastko Ciric <rc042010@mymail.pomona.edu> <rastko@stanford.edu>
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Rastko Ciric <rc042010@mymail.pomona.edu> <rciric@users.noreply.github.com>
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Rémi Gau <remi_gau@hotmail.com>
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Romain Valabregue <romain.valabregue@upmc.fr>
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Ross Blair <rblair2@stanford.edu>
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Ross Blair <rblair2@stanford.edu> <rosswilsonblair@gmail.com>

‎.maint/CONTRIBUTORS.md‎

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2020
| Feingold | Franklin | | 0000-0002-6533-2909 | Department of Psychology, Stanford University |
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| Finc | Karolina | | 0000-0002-0157-030X | Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń |
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| Frederick | Blaise B. | | 0000-0001-5832-5279 | McLean Hospital Brain Imaging Center, MA, USA |
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| Gau | Rémi | | 0000-0002-1535-9767 | Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada |
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| Groen | Iris I. A. | | 0000-0002-5536-6128 | Department of Psychology, New York University, NY, USA |
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| Gomez | Daniel E. P. | | 0000-0001-8635-021X | Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen |
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| Ghosh | Satrajit S. | | 0000-0002-5312-6729 | McGovern Institute for Brain Research, MIT, MA, USA |

‎.zenodo.json‎

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{
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"affiliation": "Florey Institute of Neuroscience and Mental Health",
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"name": "Smith, Robert E.",
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"orcid": "0000-0003-3636-4642",
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},
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"orcid": "0000-0002-0157-030X",
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{
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"affiliation": "Florey Institute of Neuroscience and Mental Health",
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"name": "Smith, Robert E.",
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"orcid": "0000-0003-3636-4642",
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"type": "Researcher"
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},
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{
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"affiliation": "Montreal Neurological Institute, McGill University",
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"name": "Bhagwat, Nikhil",
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"orcid": "0000-0001-6073-7141",
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},
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"affiliation": "Department of Psychology, New York University",
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"affiliation": "Montreal Neurological Institute, McGill University",
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{
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"affiliation": "Department of Psychology, New York University",
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"name": "Benson, Noah C.",
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"orcid": "0000-0002-2365-8265",
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"type": "Researcher"
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},
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"affiliation": "Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada",
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"affiliation": "Child Mind Institute",
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"affiliation": "Department of Psychology, University of California, Berkeley",
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‎CHANGES.rst‎

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24.0.0 (June 17, 2024)
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======================
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New feature release in the 24.0.x series.
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This release is an incremental improvement on 23.2.x, with some
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fixes for bugs discovered in the updated workflow.
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New features include separation of HTML reports by session for subjects
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with many BOLD runs, a new ``--fs-no-resume`` option to improve interoperability
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with less typical FreeSurfer directories, such as those generated by longitudinal
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FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow
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the recommendations of recent versions of BIDS.
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With thanks to Dimitri Papadopoulos, Basile Pinsard, Celine Provins, Taylor Salo
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and Wang Hao-Ting for their contributions!
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* FIX: Add "double" type to allowed DisplacementFieldTransform (#3287)
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* FIX: Require recent templateflow, select correct aparc dseg.tsv (#3256)
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* FIX: Ensure proper templates are retrieved with sloppy (#3251)
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* FIX: Delete summary from functional report when separated by sessions (#3223)
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* FIX: Support lists in bids filter file containing ``null`` or ``*`` (#3215)
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* FIX: Re-enable anat fasttrack for dataset without t1w (#3202)
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* ENH: Use BIDSURI in init_ds_boldmask_wf (#3297)
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* ENH: Add templateflow to DatasetLinks (#3267)
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* ENH: Track proximal sources of functional GIFTIs (#3263)
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* ENH: Support named derivative paths (#3264)
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* ENH: Track Sources for standard-space outputs (#3262)
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* ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (#3142)
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* ENH: Use BIDS URIs to track Sources in sidecars (#3255)
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* ENH: Ignore unselected subjects in BIDSLayoutIndexer (#3236)
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* ENH: Add metadata for motion parameters (#3245)
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* ENH: Separate anatomical and functional reports per session for densely sampled dataset (#3191)
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* ENH: Leverage T2w if available for BOLD -> anat coregistration (#3208)
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* RF: Fix ITK warp conversion to nitransforms format (#3300)
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* RF: Load report assembler from nireports (#3177)
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* DOC: Clarify ``--dvars-spike-threshold`` uses standardized DVARS (#3205)
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* TST: Update test to reflect new report generation behavior (#3210)
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* STY: Manual conversions to f-strings (#3241)
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* STY: Apply ruff/pyupgrade rule UP031 (#3280)
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* STY: Lint and style check full repository (#3221)
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* STY: Adopt ruff for linting and formatting (#3206)
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* MNT: Pin libitk 5.3 and note dependencies (#3298)
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* MNT: Upgrade ruff pre-commit, add fixing checks (#3283)
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* MNT: Complete transition from flake8/black to ruff (#3279)
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* MNT: Apply Repo-Review suggestions (#3194)
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* MNT: Verbatim copy of Apache license 2.0 (#3259)
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* MNT: Bump cryptography from 41.0.7 to 42.0.4 (#3234)
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* MNT: Drop copyright year, unused dunder fields (#3247)
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* MNT: Update environment pins (#3226)
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* MNT: Bump codecov/codecov-action from 3 to 4 (#3219)
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* DOCKER: Restore mincinfo binary (#3249)
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* CI: Move to new circle machine tags (#3248)
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* CI: Avoid ruff warning (#3244)
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* CI: Pass ruff tests (#3243)
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23.2.3 (May 20, 2024)
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=====================
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Bug fix release in the 23.2.x series.
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* FIX: Write out boldref-space brain mask with minimal level (#3292)
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23.2.2 (May 06, 2024)
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=====================
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Bug fix release in the 23.2.x series.

‎docker/files/freesurfer7.3.2-exclude.txt‎

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‎docs/benchmarks.rst‎

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.. include:: links.rst
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----------------------
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Performance benchmarks
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----------------------
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Datasets and commands
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---------------------
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Datasets
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~~~~~~~~
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+------------+----------------------------------------------------------------------------------------+
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| Dataset | Description |
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+============+========================================================================================+
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| A | 6 T1w, 3 T2w, 2 PhaseDiff, 4 SE-BOLD (195 volumes / series; total 784), 4 sbref |
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+------------+----------------------------------------------------------------------------------------+
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| B | 2 T1w, 6 PEPolar fieldmaps, 8 SE-BOLD (4274 volumes total) |
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+------------+----------------------------------------------------------------------------------------+
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fMRIPrep versions and modes
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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All commands took the form ``fmriprep sourcedata/raw . participant $OPTIONS``.
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The specific options for each version or mode are presented in the following table.
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+------------+----------------------------------------------------------------------------------------+
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| Version / | Options |
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| Mode | |
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+============+========================================================================================+
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| 23.1.4 | ``--cifti-output --output-spaces MNI152NLin2009cAsym`` |
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+------------+----------------------------------------------------------------------------------------+
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| 23.2.0a2 / | ``--level minimal --cifti-output --output-spaces MNI152NLin2009cAsym`` |
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| fit | |
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+------------+----------------------------------------------------------------------------------------+
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| 23.2.0a2 / | ``--level full --cifti-output --output-spaces MNI152NLin2009cAsym`` |
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| fit + | |
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| transform | |
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+------------+----------------------------------------------------------------------------------------+
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Machine details
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~~~~~~~~~~~~~~~
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Tests were run on a desktop machine running no other significant tests.
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* Processor: Intel i9-10900 CPU @ 2.80GHz, 20-core
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* Memory: 64GiB
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* Storage: PC801 NVMe SK hynix 2TB
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* OS: Ubuntu 22.04
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* Environment: Docker images published to https://hub.docker.com/r/nipreps/fmriprep/
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Benchmarks
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----------
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Dataset A
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~~~~~~~~~
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+------------+---------+---------+---------+---------+---------+
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| Version / | Runtime | Scratch | Scratch | Output | Output |
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| Mode | | Size | Files | Size | files |
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+============+=========+=========+=========+=========+=========+
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| 23.1.4 | 2h24m | 54.8GB | 36.8K | 2.30GB | 176 |
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+------------+---------+---------+---------+---------+---------+
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| 23.2.0a2 | 1h35m | 2.91GB | 5.89K | 602MB | 128 |
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| / fit | | | | | |
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+------------+---------+---------+---------+---------+---------+
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| 23.2.0a2 | 1h47m | 19.8GB | 10.0K | 6.37GB | 206 |
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| / fit + | | | | | |
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| transform | | | | | |
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+------------+---------+---------+---------+---------+---------+
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Dataset B
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~~~~~~~~~
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+------------+---------+---------+---------+---------+---------+
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| Version / | Runtime | Scratch | Scratch | Output | Output |
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| Mode | | Size | Files | Size | files |
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+============+=========+=========+=========+=========+=========+
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| 23.1.4 | 4h25m | 121GB | 157K | 5.10GB | 286 |
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+------------+---------+---------+---------+---------+---------+
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| 23.2.0a2 | 1h29m | 1.88GB | 12.0K | 543MB | 206 |
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| / fit | | | | | |
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+------------+---------+---------+---------+---------+---------+
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| 23.2.0a2 | 2h7m | 56.5GB | 19.8K | 14.7GB | 348 |
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| / fit + | | | | | |
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| transform | | | | | |
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+------------+---------+---------+---------+---------+---------+

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