Skip to content

Commit a49a128

Browse files
celprovcelprov
authored
Merge branch 'nipreps:master' into enh/left-right-flip-detection
2 parents 9cac594 + ff1b199 commit a49a128

25 files changed

+442
-252
lines changed

‎.circleci/ds005_fasttrack_outputs.txt

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,8 @@ sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
2323
sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
2424
sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
2525
sub-01/func
26+
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
27+
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz
2628
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
2729
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
2830
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
4143
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
4244
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
4345
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
46+
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
47+
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
4448
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
4549
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
4650
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json

‎.circleci/ds005_outputs.txt

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -43,6 +43,8 @@ sub-01/anat/sub-01_label-CSF_probseg.nii.gz
4343
sub-01/anat/sub-01_label-GM_probseg.nii.gz
4444
sub-01/anat/sub-01_label-WM_probseg.nii.gz
4545
sub-01/func
46+
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
47+
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz
4648
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
4749
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
4850
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
6163
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
6264
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
6365
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
66+
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
67+
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
6468
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
6569
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
6670
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json

‎.circleci/ds005_partial_fasttrack_outputs.txt

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -51,6 +51,8 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
5151
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
5252
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
5353
sub-01/func
54+
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
55+
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
5456
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
5557
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
5658
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json

‎.circleci/ds005_partial_outputs.txt

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -73,6 +73,8 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
7373
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
7474
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
7575
sub-01/func
76+
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
77+
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
7678
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
7779
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
7880
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json

‎.mailmap

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ Alejandro de la Vega <aleph4@gmail.com> delavega4
55
Anibal Sólon Heinsfeld <anibalsolon@gmail.com>
66
Asier Erramuzpe <asier.erramuzpe@gmail.com>
77
Basile Pinsard <basile.pinsard@umontreal.ca>
8-
Basile Pinsard <basile.pinsard@umontreal.ca> basile <basile.pinsard@gmail.com>
8+
Basile Pinsard <basile.pinsard@umontreal.ca> <basile.pinsard@gmail.com>
99
Basile Pinsard <basile.pinsard@umontreal.ca> <bpinsard@imed.jussieu.fr>
1010
Blaise Frederick <blaise.frederick@gmail.com>
1111
Blaise Frederick <blaise.frederick@gmail.com> bbfrederick <blaise.frederick@gmail.com>
@@ -60,6 +60,7 @@ Pablo Velasco <pablo.velasco@nyu.edu>
6060
Rastko Ciric <rc042010@mymail.pomona.edu>
6161
Rastko Ciric <rc042010@mymail.pomona.edu> <rastko@stanford.edu>
6262
Rastko Ciric <rc042010@mymail.pomona.edu> <rciric@users.noreply.github.com>
63+
Rémi Gau <remi_gau@hotmail.com>
6364
Romain Valabregue <romain.valabregue@upmc.fr>
6465
Ross Blair <rblair2@stanford.edu>
6566
Ross Blair <rblair2@stanford.edu> <rosswilsonblair@gmail.com>

‎.maint/CONTRIBUTORS.md

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,7 @@ Before every release, unlisted contributors will be invited again to add their n
2020
| Feingold | Franklin | | 0000-0002-6533-2909 | Department of Psychology, Stanford University |
2121
| Finc | Karolina | | 0000-0002-0157-030X | Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń |
2222
| Frederick | Blaise B. | | 0000-0001-5832-5279 | McLean Hospital Brain Imaging Center, MA, USA |
23+
| Gau | Rémi | | 0000-0002-1535-9767 | Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada |
2324
| Groen | Iris I. A. | | 0000-0002-5536-6128 | Department of Psychology, New York University, NY, USA |
2425
| Gomez | Daniel E. P. | | 0000-0001-8635-021X | Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen |
2526
| Ghosh | Satrajit S. | | 0000-0002-5312-6729 | McGovern Institute for Brain Research, MIT, MA, USA |

‎.zenodo.json

Lines changed: 41 additions & 35 deletions
Original file line numberDiff line numberDiff line change
@@ -14,12 +14,6 @@
1414
"orcid": "0000-0003-3030-6580",
1515
"type": "Researcher"
1616
},
17-
{
18-
"affiliation": "Florey Institute of Neuroscience and Mental Health",
19-
"name": "Smith, Robert E.",
20-
"orcid": "0000-0003-3636-4642",
21-
"type": "Researcher"
22-
},
2317
{
2418
"affiliation": "Neurospin, CEA",
2519
"name": "Papadopoulos, Dimitri",
@@ -32,6 +26,12 @@
3226
"orcid": "0000-0002-0157-030X",
3327
"type": "Researcher"
3428
},
29+
{
30+
"affiliation": "Florey Institute of Neuroscience and Mental Health",
31+
"name": "Smith, Robert E.",
32+
"orcid": "0000-0003-3636-4642",
33+
"type": "Researcher"
34+
},
3535
{
3636
"affiliation": "Department of Psychology, Stanford University",
3737
"name": "Feingold, Franklin",
@@ -44,22 +44,16 @@
4444
"orcid": "0000-0001-6377-3885",
4545
"type": "Researcher"
4646
},
47-
{
48-
"affiliation": "Montreal Neurological Institute, McGill University",
49-
"name": "Bhagwat, Nikhil",
50-
"orcid": "0000-0001-6073-7141",
51-
"type": "Researcher"
52-
},
5347
{
5448
"affiliation": "Dartmouth College: Hanover, NH, United States",
5549
"name": "Halchenko, Yaroslav O.",
5650
"orcid": "0000-0003-3456-2493",
5751
"type": "Researcher"
5852
},
5953
{
60-
"affiliation": "Department of Psychology, New York University",
61-
"name": "Benson, Noah C.",
62-
"orcid": "0000-0002-2365-8265",
54+
"affiliation": "Montreal Neurological Institute, McGill University",
55+
"name": "Bhagwat, Nikhil",
56+
"orcid": "0000-0001-6073-7141",
6357
"type": "Researcher"
6458
},
6559
{
@@ -80,16 +74,22 @@
8074
"orcid": "0000-0001-5504-8579",
8175
"type": "Researcher"
8276
},
77+
{
78+
"affiliation": "Department of Psychology, New York University",
79+
"name": "Benson, Noah C.",
80+
"orcid": "0000-0002-2365-8265",
81+
"type": "Researcher"
82+
},
8383
{
8484
"affiliation": "Machine Learning Team, National Institute of Mental Health, USA",
8585
"name": "Nielson, Dylan M.",
8686
"orcid": "0000-0003-4613-6643",
8787
"type": "Researcher"
8888
},
8989
{
90-
"affiliation": "Child Mind Institute",
91-
"name": "Heinsfeld, Anibal S.",
92-
"orcid": "0000-0002-2050-0614",
90+
"affiliation": "Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada",
91+
"name": "Gau, Rémi",
92+
"orcid": "0000-0002-1535-9767",
9393
"type": "Researcher"
9494
},
9595
{
@@ -105,15 +105,9 @@
105105
"type": "Researcher"
106106
},
107107
{
108-
"affiliation": "Department of Psychology, University of California, Berkeley",
109-
"name": "Lurie, Daniel J.",
110-
"orcid": "0000-0001-8012-6399",
111-
"type": "Researcher"
112-
},
113-
{
114-
"affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
115-
"name": "Erramuzpe, Asier",
116-
"orcid": "0000-0002-9402-2184",
108+
"affiliation": "Child Mind Institute",
109+
"name": "Heinsfeld, Anibal S.",
110+
"orcid": "0000-0002-2050-0614",
117111
"type": "Researcher"
118112
},
119113
{
@@ -123,9 +117,15 @@
123117
"type": "Researcher"
124118
},
125119
{
126-
"affiliation": "Department of Psychology, Stanford University",
127-
"name": "Wexler, Joseph B.",
128-
"orcid": "0000-0001-6424-8740",
120+
"affiliation": "Department of Psychology, University of California, Berkeley",
121+
"name": "Lurie, Daniel J.",
122+
"orcid": "0000-0001-8012-6399",
123+
"type": "Researcher"
124+
},
125+
{
126+
"affiliation": "Computational Neuroimaging Lab, BioCruces Health Research Institute",
127+
"name": "Erramuzpe, Asier",
128+
"orcid": "0000-0002-9402-2184",
129129
"type": "Researcher"
130130
},
131131
{
@@ -140,6 +140,12 @@
140140
"orcid": "0000-0002-5740-9451",
141141
"type": "Researcher"
142142
},
143+
{
144+
"affiliation": "Department of Psychology, Stanford University",
145+
"name": "Wexler, Joseph B.",
146+
"orcid": "0000-0001-6424-8740",
147+
"type": "Researcher"
148+
},
143149
{
144150
"affiliation": "Dartmouth College: Hanover, NH, United States",
145151
"name": "Ma, Feilong",
@@ -298,16 +304,16 @@
298304
}
299305
],
300306
"creators": [
301-
{
302-
"affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
303-
"name": "Esteban, Oscar",
304-
"orcid": "0000-0001-8435-6191"
305-
},
306307
{
307308
"affiliation": "Department of Psychology, Stanford University",
308309
"name": "Markiewicz, Christopher J.",
309310
"orcid": "0000-0002-6533-164X"
310311
},
312+
{
313+
"affiliation": "Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland",
314+
"name": "Esteban, Oscar",
315+
"orcid": "0000-0001-8435-6191"
316+
},
311317
{
312318
"affiliation": "Department of Psychology, Stanford University",
313319
"name": "Goncalves, Mathias",

‎CHANGES.rst

Lines changed: 67 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,70 @@
1+
24.0.0 (June 17, 2024)
2+
======================
3+
4+
New feature release in the 24.0.x series.
5+
6+
This release is an incremental improvement on 23.2.x, with some
7+
fixes for bugs discovered in the updated workflow.
8+
9+
New features include separation of HTML reports by session for subjects
10+
with many BOLD runs, a new ``--fs-no-resume`` option to improve interoperability
11+
with less typical FreeSurfer directories, such as those generated by longitudinal
12+
FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow
13+
the recommendations of recent versions of BIDS.
14+
15+
With thanks to Dimitri Papadopoulos, Basile Pinsard, Celine Provins, Taylor Salo
16+
and Wang Hao-Ting for their contributions!
17+
18+
* FIX: Add "double" type to allowed DisplacementFieldTransform (#3287)
19+
* FIX: Require recent templateflow, select correct aparc dseg.tsv (#3256)
20+
* FIX: Ensure proper templates are retrieved with sloppy (#3251)
21+
* FIX: Delete summary from functional report when separated by sessions (#3223)
22+
* FIX: Support lists in bids filter file containing ``null`` or ``*`` (#3215)
23+
* FIX: Re-enable anat fasttrack for dataset without t1w (#3202)
24+
* ENH: Use BIDSURI in init_ds_boldmask_wf (#3297)
25+
* ENH: Add templateflow to DatasetLinks (#3267)
26+
* ENH: Track proximal sources of functional GIFTIs (#3263)
27+
* ENH: Support named derivative paths (#3264)
28+
* ENH: Track Sources for standard-space outputs (#3262)
29+
* ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (#3142)
30+
* ENH: Use BIDS URIs to track Sources in sidecars (#3255)
31+
* ENH: Ignore unselected subjects in BIDSLayoutIndexer (#3236)
32+
* ENH: Add metadata for motion parameters (#3245)
33+
* ENH: Separate anatomical and functional reports per session for densely sampled dataset (#3191)
34+
* ENH: Leverage T2w if available for BOLD -> anat coregistration (#3208)
35+
* RF: Fix ITK warp conversion to nitransforms format (#3300)
36+
* RF: Load report assembler from nireports (#3177)
37+
* DOC: Clarify ``--dvars-spike-threshold`` uses standardized DVARS (#3205)
38+
* TST: Update test to reflect new report generation behavior (#3210)
39+
* STY: Manual conversions to f-strings (#3241)
40+
* STY: Apply ruff/pyupgrade rule UP031 (#3280)
41+
* STY: Lint and style check full repository (#3221)
42+
* STY: Adopt ruff for linting and formatting (#3206)
43+
* MNT: Pin libitk 5.3 and note dependencies (#3298)
44+
* MNT: Upgrade ruff pre-commit, add fixing checks (#3283)
45+
* MNT: Complete transition from flake8/black to ruff (#3279)
46+
* MNT: Apply Repo-Review suggestions (#3194)
47+
* MNT: Verbatim copy of Apache license 2.0 (#3259)
48+
* MNT: Bump cryptography from 41.0.7 to 42.0.4 (#3234)
49+
* MNT: Drop copyright year, unused dunder fields (#3247)
50+
* MNT: Update environment pins (#3226)
51+
* MNT: Bump codecov/codecov-action from 3 to 4 (#3219)
52+
* DOCKER: Restore mincinfo binary (#3249)
53+
* CI: Move to new circle machine tags (#3248)
54+
* CI: Avoid ruff warning (#3244)
55+
* CI: Pass ruff tests (#3243)
56+
57+
58+
23.2.3 (May 20, 2024)
59+
=====================
60+
Bug fix release in the 23.2.x series.
61+
62+
Writes brain masks in ``space-boldref`` with ``--level minimal``,
63+
bringing behavior in line with documentation.
64+
65+
* FIX: Write out boldref-space brain mask with minimal level (#3292)
66+
67+
168
23.2.2 (May 06, 2024)
269
=====================
370
Bug fix release in the 23.2.x series.

‎docker/files/freesurfer7.3.2-exclude.txt

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -797,7 +797,6 @@ freesurfer/mni/bin/mincmakevector
797797
freesurfer/mni/bin/mincmath
798798
freesurfer/mni/bin/minc_modify_header
799799
freesurfer/mni/bin/mincpik
800-
freesurfer/mni/bin/mincreshape
801800
freesurfer/mni/bin/mincstats
802801
freesurfer/mni/bin/minctoecat
803802
freesurfer/mni/bin/minctoraw

‎docs/benchmarks.rst

Lines changed: 86 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,86 @@
1+
.. include:: links.rst
2+
3+
----------------------
4+
Performance benchmarks
5+
----------------------
6+
7+
Datasets and commands
8+
---------------------
9+
10+
Datasets
11+
~~~~~~~~
12+
+------------+----------------------------------------------------------------------------------------+
13+
| Dataset | Description |
14+
+============+========================================================================================+
15+
| A | 6 T1w, 3 T2w, 2 PhaseDiff, 4 SE-BOLD (195 volumes / series; total 784), 4 sbref |
16+
+------------+----------------------------------------------------------------------------------------+
17+
| B | 2 T1w, 6 PEPolar fieldmaps, 8 SE-BOLD (4274 volumes total) |
18+
+------------+----------------------------------------------------------------------------------------+
19+
20+
fMRIPrep versions and modes
21+
~~~~~~~~~~~~~~~~~~~~~~~~~~~
22+
23+
All commands took the form ``fmriprep sourcedata/raw . participant $OPTIONS``.
24+
The specific options for each version or mode are presented in the following table.
25+
26+
+------------+----------------------------------------------------------------------------------------+
27+
| Version / | Options |
28+
| Mode | |
29+
+============+========================================================================================+
30+
| 23.1.4 | ``--cifti-output --output-spaces MNI152NLin2009cAsym`` |
31+
+------------+----------------------------------------------------------------------------------------+
32+
| 23.2.0a2 / | ``--level minimal --cifti-output --output-spaces MNI152NLin2009cAsym`` |
33+
| fit | |
34+
+------------+----------------------------------------------------------------------------------------+
35+
| 23.2.0a2 / | ``--level full --cifti-output --output-spaces MNI152NLin2009cAsym`` |
36+
| fit + | |
37+
| transform | |
38+
+------------+----------------------------------------------------------------------------------------+
39+
40+
Machine details
41+
~~~~~~~~~~~~~~~
42+
43+
Tests were run on a desktop machine running no other significant tests.
44+
45+
* Processor: Intel i9-10900 CPU @ 2.80GHz, 20-core
46+
* Memory: 64GiB
47+
* Storage: PC801 NVMe SK hynix 2TB
48+
* OS: Ubuntu 22.04
49+
* Environment: Docker images published to https://hub.docker.com/r/nipreps/fmriprep/
50+
51+
Benchmarks
52+
----------
53+
54+
Dataset A
55+
~~~~~~~~~
56+
57+
+------------+---------+---------+---------+---------+---------+
58+
| Version / | Runtime | Scratch | Scratch | Output | Output |
59+
| Mode | | Size | Files | Size | files |
60+
+============+=========+=========+=========+=========+=========+
61+
| 23.1.4 | 2h24m | 54.8GB | 36.8K | 2.30GB | 176 |
62+
+------------+---------+---------+---------+---------+---------+
63+
| 23.2.0a2 | 1h35m | 2.91GB | 5.89K | 602MB | 128 |
64+
| / fit | | | | | |
65+
+------------+---------+---------+---------+---------+---------+
66+
| 23.2.0a2 | 1h47m | 19.8GB | 10.0K | 6.37GB | 206 |
67+
| / fit + | | | | | |
68+
| transform | | | | | |
69+
+------------+---------+---------+---------+---------+---------+
70+
71+
Dataset B
72+
~~~~~~~~~
73+
74+
+------------+---------+---------+---------+---------+---------+
75+
| Version / | Runtime | Scratch | Scratch | Output | Output |
76+
| Mode | | Size | Files | Size | files |
77+
+============+=========+=========+=========+=========+=========+
78+
| 23.1.4 | 4h25m | 121GB | 157K | 5.10GB | 286 |
79+
+------------+---------+---------+---------+---------+---------+
80+
| 23.2.0a2 | 1h29m | 1.88GB | 12.0K | 543MB | 206 |
81+
| / fit | | | | | |
82+
+------------+---------+---------+---------+---------+---------+
83+
| 23.2.0a2 | 2h7m | 56.5GB | 19.8K | 14.7GB | 348 |
84+
| / fit + | | | | | |
85+
| transform | | | | | |
86+
+------------+---------+---------+---------+---------+---------+

0 commit comments

Comments
 (0)