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Robustify fMRIprep hack #4

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adswa merged 1 commit from robustify-fmriprep into main 2022-05-04 15:19:53 +00:00
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1 changed files with 2 additions and 2 deletions
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bootstrap_forrest_fmriprep.sh
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@ -114,7 +114,7 @@ mkdir -p .git/tmp/wdir
# After job completion, the jsons will be restored.
# See https://github.com/bids-standard/pybids/issues/631 for more information.
find inputs/data -mindepth 2 -name '*.json' -a ! -wholename "$subid" | sed -e "p;s/json/xyz/" | xargs -n2 mv
find inputs/data -mindepth 2 -name '*.json' -a ! -wholename "$subid" | sed -e "p;s/json/xyz/" | xargs --no-run-if-empty -n2 mv
# execute fmriprep. Its runscript is available as /singularity within the
# container. Custom fmriprep parametrization can be done here.
@ -124,7 +124,7 @@ find inputs/data -mindepth 2 -name '*.json' -a ! -wholename "$subid" | sed -e "p
# restore the jsons we have moved out of the way
find inputs/data -mindepth 2 -name '*.xyz' -a ! -wholename "$subid" | sed -e "p;s/xyz/json/" | xargs -n2 mv
find inputs/data -mindepth 2 -name '*.xyz' -a ! -wholename "$subid" | sed -e "p;s/xyz/json/" | xargs --no-run-if-empty -n2 mv
EOT