Merge branch 'nipreps:master' into enh/left-right-flip-detection

.circleci/ds005_fasttrack_outputs.txt

@@ -23,6 +23,8 @@ sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/func
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json
@@ -41,6 +43,8 @@ sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.fun
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json

.circleci/ds005_outputs.txt

@@ -43,6 +43,8 @@ sub-01/anat/sub-01_label-CSF_probseg.nii.gz
 sub-01/anat/sub-01_label-GM_probseg.nii.gz
 sub-01/anat/sub-01_label-WM_probseg.nii.gz
 sub-01/func
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
+sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json
@@ -61,6 +63,8 @@ sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.fun
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json

.circleci/ds005_partial_fasttrack_outputs.txt

@@ -51,6 +51,8 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 sub-01/func
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json

.circleci/ds005_partial_outputs.txt

@@ -73,6 +73,8 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 sub-01/func
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
+sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json

.mailmap

@@ -5,7 +5,7 @@ Alejandro de la Vega <[email protected]> delavega4
 Anibal Sólon Heinsfeld <[email protected]>
 Asier Erramuzpe <[email protected]>
 Basile Pinsard <[email protected]>
-Basile Pinsard <[email protected]> basile <[email protected]>
+Basile Pinsard <[email protected]> <[email protected]>
 Basile Pinsard <[email protected]> <[email protected]>
 Blaise Frederick <[email protected]>
 Blaise Frederick <[email protected]> bbfrederick <[email protected]>
@@ -60,6 +60,7 @@ Pablo Velasco <[email protected]>
 Rastko Ciric <[email protected]>
 Rastko Ciric <[email protected]> <[email protected]>
 Rastko Ciric <[email protected]> <[email protected]>
+Rémi Gau <[email protected]>
 Romain Valabregue <[email protected]>
 Ross Blair <[email protected]>
 Ross Blair <[email protected]> <[email protected]>

.maint/CONTRIBUTORS.md

@@ -20,6 +20,7 @@ Before every release, unlisted contributors will be invited again to add their n
 | Feingold          | Franklin     |  | 0000-0002-6533-2909 | Department of Psychology, Stanford University                                                                                                |
 | Finc              | Karolina     |  | 0000-0002-0157-030X | Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń                                                    |
 | Frederick         | Blaise B.    |  | 0000-0001-5832-5279 | McLean Hospital Brain Imaging Center, MA, USA                                                                                                |
+| Gau               | Rémi        |  | 0000-0002-1535-9767 | Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada             |
 | Groen             | Iris I. A.   |  | 0000-0002-5536-6128 | Department of Psychology, New York University, NY, USA                                                                                       |
 | Gomez             | Daniel E. P. |  | 0000-0001-8635-021X | Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen                                                            |
 | Ghosh             | Satrajit S.  |  | 0000-0002-5312-6729 | McGovern Institute for Brain Research, MIT, MA, USA                                                                                          |

.zenodo.json

@@ -14,12 +14,6 @@
       "orcid": "0000-0003-3030-6580",
       "type": "Researcher"
     },
-    {
-      "affiliation": "Florey Institute of Neuroscience and Mental Health",
-      "name": "Smith, Robert E.",
-      "orcid": "0000-0003-3636-4642",
-      "type": "Researcher"
-    },
     {
       "affiliation": "Neurospin, CEA",
       "name": "Papadopoulos, Dimitri",
@@ -32,6 +26,12 @@
       "orcid": "0000-0002-0157-030X",
       "type": "Researcher"
     },
+    {
+      "affiliation": "Florey Institute of Neuroscience and Mental Health",
+      "name": "Smith, Robert E.",
+      "orcid": "0000-0003-3636-4642",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Feingold, Franklin",
@@ -44,22 +44,16 @@
       "orcid": "0000-0001-6377-3885",
       "type": "Researcher"
     },
-    {
-      "affiliation": "Montreal Neurological Institute, McGill University",
-      "name": "Bhagwat, Nikhil",
-      "orcid": "0000-0001-6073-7141",
-      "type": "Researcher"
-    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Halchenko, Yaroslav O.",
       "orcid": "0000-0003-3456-2493",
       "type": "Researcher"
     },
     {
-      "affiliation": "Department of Psychology, New York University",
-      "name": "Benson, Noah C.",
-      "orcid": "0000-0002-2365-8265",
+      "affiliation": "Montreal Neurological Institute, McGill University",
+      "name": "Bhagwat, Nikhil",
+      "orcid": "0000-0001-6073-7141",
       "type": "Researcher"
     },
     {
@@ -80,16 +74,22 @@
       "orcid": "0000-0001-5504-8579",
       "type": "Researcher"
     },
+    {
+      "affiliation": "Department of Psychology, New York University",
+      "name": "Benson, Noah C.",
+      "orcid": "0000-0002-2365-8265",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Machine Learning Team, National Institute of Mental Health, USA",
       "name": "Nielson, Dylan M.",
       "orcid": "0000-0003-4613-6643",
       "type": "Researcher"
     },
     {
-      "affiliation": "Child Mind Institute",
-      "name": "Heinsfeld, Anibal S.",
-      "orcid": "0000-0002-2050-0614",
+      "affiliation": "Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada",
+      "name": "Gau, Rémi",
+      "orcid": "0000-0002-1535-9767",
       "type": "Researcher"
     },
     {
@@ -105,15 +105,9 @@
       "type": "Researcher"
     },
     {
-      "affiliation": "Department of Psychology, University of California, Berkeley",
-      "name": "Lurie, Daniel J.",
-      "orcid": "0000-0001-8012-6399",
-      "type": "Researcher"
-    },
-    {
-      "affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
-      "name": "Erramuzpe, Asier",
-      "orcid": "0000-0002-9402-2184",
+      "affiliation": "Child Mind Institute",
+      "name": "Heinsfeld, Anibal S.",
+      "orcid": "0000-0002-2050-0614",
       "type": "Researcher"
     },
     {
@@ -123,9 +117,15 @@
       "type": "Researcher"
     },
     {
-      "affiliation": "Department of Psychology, Stanford University",
-      "name": "Wexler, Joseph B.",
-      "orcid": "0000-0001-6424-8740",
+      "affiliation": "Department of Psychology, University of California, Berkeley",
+      "name": "Lurie, Daniel J.",
+      "orcid": "0000-0001-8012-6399",
+      "type": "Researcher"
+    },
+    {
+      "affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
+      "name": "Erramuzpe, Asier",
+      "orcid": "0000-0002-9402-2184",
       "type": "Researcher"
     },
     {
@@ -140,6 +140,12 @@
       "orcid": "0000-0002-5740-9451",
       "type": "Researcher"
     },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Wexler, Joseph B.",
+      "orcid": "0000-0001-6424-8740",
+      "type": "Researcher"
+    },
     {
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "name": "Ma, Feilong",
@@ -298,16 +304,16 @@
     }
   ],
   "creators": [
-    {
-      "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
-      "name": "Esteban, Oscar",
-      "orcid": "0000-0001-8435-6191"
-    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Markiewicz, Christopher J.",
       "orcid": "0000-0002-6533-164X"
     },
+    {
+      "affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
+      "name": "Esteban, Oscar",
+      "orcid": "0000-0001-8435-6191"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Goncalves, Mathias",

CHANGES.rst

@@ -1,3 +1,70 @@
+24.0.0 (June 17, 2024)
+======================
+
+New feature release in the 24.0.x series.
+
+This release is an incremental improvement on 23.2.x, with some
+fixes for bugs discovered in the updated workflow.
+
+New features include separation of HTML reports by session for subjects
+with many BOLD runs, a new ``--fs-no-resume`` option to improve interoperability
+with less typical FreeSurfer directories, such as those generated by longitudinal
+FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow
+the recommendations of recent versions of BIDS.
+
+With thanks to Dimitri Papadopoulos, Basile Pinsard, Celine Provins, Taylor Salo
+and Wang Hao-Ting for their contributions!
+
+* FIX: Add "double" type to allowed DisplacementFieldTransform (#3287)
+* FIX: Require recent templateflow, select correct aparc dseg.tsv (#3256)
+* FIX: Ensure proper templates are retrieved with sloppy (#3251)
+* FIX: Delete summary from functional report when separated by sessions (#3223)
+* FIX: Support lists in bids filter file containing ``null`` or ``*`` (#3215)
+* FIX: Re-enable anat fasttrack for dataset without t1w (#3202)
+* ENH: Use BIDSURI in init_ds_boldmask_wf (#3297)
+* ENH: Add templateflow to DatasetLinks (#3267)
+* ENH: Track proximal sources of functional GIFTIs (#3263)
+* ENH: Support named derivative paths (#3264)
+* ENH: Track Sources for standard-space outputs (#3262)
+* ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (#3142)
+* ENH: Use BIDS URIs to track Sources in sidecars (#3255)
+* ENH: Ignore unselected subjects in BIDSLayoutIndexer (#3236)
+* ENH: Add metadata for motion parameters (#3245)
+* ENH: Separate anatomical and functional reports per session for densely sampled dataset (#3191)
+* ENH: Leverage T2w if available for BOLD -> anat coregistration (#3208)
+* RF: Fix ITK warp conversion to nitransforms format (#3300)
+* RF: Load report assembler from nireports (#3177)
+* DOC: Clarify ``--dvars-spike-threshold`` uses standardized DVARS (#3205)
+* TST: Update test to reflect new report generation behavior (#3210)
+* STY: Manual conversions to f-strings (#3241)
+* STY: Apply ruff/pyupgrade rule UP031 (#3280)
+* STY: Lint and style check full repository (#3221)
+* STY: Adopt ruff for linting and formatting (#3206)
+* MNT: Pin libitk 5.3 and note dependencies (#3298)
+* MNT: Upgrade ruff pre-commit, add fixing checks (#3283)
+* MNT: Complete transition from flake8/black to ruff (#3279)
+* MNT: Apply Repo-Review suggestions (#3194)
+* MNT: Verbatim copy of Apache license 2.0 (#3259)
+* MNT: Bump cryptography from 41.0.7 to 42.0.4 (#3234)
+* MNT: Drop copyright year, unused dunder fields (#3247)
+* MNT: Update environment pins (#3226)
+* MNT: Bump codecov/codecov-action from 3 to 4 (#3219)
+* DOCKER: Restore mincinfo binary (#3249)
+* CI: Move to new circle machine tags (#3248)
+* CI: Avoid ruff warning (#3244)
+* CI: Pass ruff tests (#3243)
+
+
+23.2.3 (May 20, 2024)
+=====================
+Bug fix release in the 23.2.x series.
+
+Writes brain masks in ``space-boldref`` with ``--level minimal``,
+bringing behavior in line with documentation.
+
+* FIX: Write out boldref-space brain mask with minimal level (#3292)
+
+
 23.2.2 (May 06, 2024)
 =====================
 Bug fix release in the 23.2.x series.

docker/files/freesurfer7.3.2-exclude.txt

@@ -797,7 +797,6 @@ freesurfer/mni/bin/mincmakevector
 freesurfer/mni/bin/mincmath
 freesurfer/mni/bin/minc_modify_header
 freesurfer/mni/bin/mincpik
-freesurfer/mni/bin/mincreshape
 freesurfer/mni/bin/mincstats
 freesurfer/mni/bin/minctoecat
 freesurfer/mni/bin/minctoraw

docs/benchmarks.rst

@@ -0,0 +1,86 @@
+.. include:: links.rst
+
+----------------------
+Performance benchmarks
+----------------------
+
+Datasets and commands
+---------------------
+
+Datasets
+~~~~~~~~
++------------+----------------------------------------------------------------------------------------+
+| Dataset    | Description                                                                            |
++============+========================================================================================+
+| A          | 6 T1w, 3 T2w, 2 PhaseDiff, 4 SE-BOLD (195 volumes / series; total 784), 4 sbref        |
++------------+----------------------------------------------------------------------------------------+
+| B          | 2 T1w, 6 PEPolar fieldmaps, 8 SE-BOLD (4274 volumes total)                             |
++------------+----------------------------------------------------------------------------------------+
+
+fMRIPrep versions and modes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+All commands took the form ``fmriprep sourcedata/raw . participant $OPTIONS``.
+The specific options for each version or mode are presented in the following table.
+
++------------+----------------------------------------------------------------------------------------+
+| Version /  | Options                                                                                |
+| Mode       |                                                                                        |
++============+========================================================================================+
+| 23.1.4     | ``--cifti-output --output-spaces MNI152NLin2009cAsym``                                 |
++------------+----------------------------------------------------------------------------------------+
+| 23.2.0a2 / | ``--level minimal --cifti-output --output-spaces MNI152NLin2009cAsym``                 |
+| fit        |                                                                                        |
++------------+----------------------------------------------------------------------------------------+
+| 23.2.0a2 / | ``--level full --cifti-output --output-spaces MNI152NLin2009cAsym``                    |
+| fit +      |                                                                                        |
+| transform  |                                                                                        |
++------------+----------------------------------------------------------------------------------------+
+
+Machine details
+~~~~~~~~~~~~~~~
+
+Tests were run on a desktop machine running no other significant tests.
+
+* Processor: Intel i9-10900 CPU @ 2.80GHz, 20-core
+* Memory: 64GiB
+* Storage: PC801 NVMe SK hynix 2TB
+* OS: Ubuntu 22.04
+* Environment: Docker images published to https://hub.docker.com/r/nipreps/fmriprep/
+
+Benchmarks
+----------
+
+Dataset A
+~~~~~~~~~
+
++------------+---------+---------+---------+---------+---------+
+| Version /  | Runtime | Scratch | Scratch | Output  | Output  |
+| Mode       |         | Size    | Files   | Size    | files   |
++============+=========+=========+=========+=========+=========+
+| 23.1.4     | 2h24m   | 54.8GB  | 36.8K   | 2.30GB  | 176     |
++------------+---------+---------+---------+---------+---------+
+| 23.2.0a2   | 1h35m   | 2.91GB  | 5.89K   | 602MB   | 128     |
+| / fit      |         |         |         |         |         |
++------------+---------+---------+---------+---------+---------+
+| 23.2.0a2   | 1h47m   | 19.8GB  | 10.0K   | 6.37GB  | 206     |
+| / fit +    |         |         |         |         |         |
+| transform  |         |         |         |         |         |
++------------+---------+---------+---------+---------+---------+
+
+Dataset B
+~~~~~~~~~
+
++------------+---------+---------+---------+---------+---------+
+| Version /  | Runtime | Scratch | Scratch | Output  | Output  |
+| Mode       |         | Size    | Files   | Size    | files   |
++============+=========+=========+=========+=========+=========+
+| 23.1.4     | 4h25m   | 121GB   | 157K    | 5.10GB  | 286     |
++------------+---------+---------+---------+---------+---------+
+| 23.2.0a2   | 1h29m   | 1.88GB  | 12.0K   | 543MB   | 206     |
+| / fit      |         |         |         |         |         |
++------------+---------+---------+---------+---------+---------+
+| 23.2.0a2   | 2h7m    | 56.5GB  | 19.8K   | 14.7GB  | 348     |
+| / fit +    |         |         |         |         |         |
+| transform  |         |         |         |         |         |
++------------+---------+---------+---------+---------+---------+