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Final revisions for next branch #3134

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merged 17 commits into from
Nov 19, 2023
Merged

Final revisions for next branch #3134

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12e4b19
MNT: Update NodeJS, svgo and bids-validator
effigies Nov 14, 2023
67ff4d6
FIX: Pass bold file to ds_fmapreg_wf to get correct naming
effigies Nov 15, 2023
a205037
CI: Remove legacy outputs, update ds005 fasttrack outputs
effigies Nov 15, 2023
2ff1ddc
FIX: Add ds054 and ds210 fastrack outputs [no fasttrack]
effigies Nov 15, 2023
8fd5fbe
CFG: Remove hacks intended to ease development
effigies Nov 15, 2023
195521d
RF: Remove old copy of _create_mem_gb
effigies Nov 15, 2023
d84fc31
DOC: Add docstring for init_bold_volumetric_resample_wf
effigies Nov 15, 2023
a549a33
CI: Update full output listings
effigies Nov 15, 2023
2203620
RF: Remove reporting from coregistration workflows
effigies Nov 15, 2023
9f29894
RF: Remove unused bold_t1_trans_wf
effigies Nov 15, 2023
f71fb1d
RF: Drop VolumeToSurfaceMapping output weights
effigies Nov 15, 2023
be5ba8f
CI: Restore expected outputs checks
effigies Nov 15, 2023
d2bb045
FIX: Use msmsulc registration
effigies Nov 15, 2023
4d35109
RF: Listify and sort BOLD series by EchoTime once [no fasttrack]
effigies Nov 16, 2023
fbbfbd0
ENH: Restore STC reporting to summary
effigies Nov 17, 2023
b323eb0
FIX: Pass fmriprep output directory to anatomical workflow
effigies Nov 17, 2023
4647b6e
FIX: Correctly generate resampling reference, pass to downstream resa…
effigies Nov 17, 2023
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25 changes: 23 additions & 2 deletions .circleci/config.yml
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Expand Up @@ -87,9 +87,30 @@ _setup_fmriprep_docker: &setup_fmriprep_docker
pip install --upgrade /tmp/src/fmriprep/wrapper/

_check_outputs: &check_outputs
name: Show outputs of fMRIPrep run
name: Check outputs of fMRIPrep run
command: |
find /tmp/${DATASET}/${SUBDIR:-fmriprep} \( -path '*/figures' -o -path '*/log' -o -path '*/sourcedata' \) -prune -o -name "*" -print | cut -d/ -f 5- | sort
set +e -x
mkdir -p /tmp/${DATASET}/test
find /tmp/${DATASET}/${SUBDIR:-fmriprep} \
\( -path '*/figures' -o -path '*/log' -o -path '*/sourcedata' \) \
-prune -o -name "*" -print | cut -d/ -f 5- | sort > /tmp/${DATASET}/test/outputs.out

FASTTRACK_OUTPUTS="${DATASET}${VARIANT}_fasttrack_outputs.txt"
FULL_OUTPUTS="${DATASET}${VARIANT}_outputs.txt"
RET=1
if [ ! -f /tmp/.nofasttrack ]; then
echo "Checking fasttrack..."
sort /tmp/src/fmriprep/.circleci/${FASTTRACK_OUTPUTS} > /tmp/${DATASET}/test/fasttrack.out
diff /tmp/${DATASET}/test/{fasttrack,outputs}.out
RET=$?
fi
if [ $RET -ne 0 ]; then
echo "Checking full..."
sort /tmp/src/fmriprep/.circleci/${FULL_OUTPUTS} > /tmp/${DATASET}/test/full.out
diff /tmp/${DATASET}/test/{full,outputs}.out
RET=$?
fi
exit $RET

version: 2.1
aliases:
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67 changes: 0 additions & 67 deletions .circleci/ds005_bids_outputs.txt
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70 changes: 70 additions & 0 deletions .circleci/ds005_fasttrack_outputs.txt
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@@ -0,0 +1,70 @@

.bidsignore
dataset_description.json
desc-aparcaseg_dseg.tsv
desc-aseg_dseg.tsv
logs
logs/CITATION.bib
logs/CITATION.html
logs/CITATION.md
logs/CITATION.tex
sub-01
sub-01/anat
sub-01/anat/sub-01_desc-ribbon_mask.json
sub-01/anat/sub-01_desc-ribbon_mask.nii.gz
sub-01/anat/sub-01_hemi-L_desc-preproc_sphere.surf.gii
sub-01/anat/sub-01_hemi-L_desc-preproc_white.surf.gii
sub-01/anat/sub-01_hemi-L_desc-reg_sphere.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_desc-preproc_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_desc-preproc_white.surf.gii
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
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsnative_bold.func.gii
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsnative_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii
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
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsnative_bold.func.gii
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsnative_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.func.gii
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.func.gii
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.json
sub-01.html
76 changes: 0 additions & 76 deletions .circleci/ds005_legacy_outputs.txt
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