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- #!/bin/bash
- subid=$1
- # create workdir for fmriprep inside the dataset to simplify singularity call
- # PWD will be available in the container
- mkdir -p .git/tmp/wdir
- # pybids (inside fmriprep) will try to read all JSON files in a dataset. In case
- # of a recomputation, JSON files of other subjects can be dangling symlinks.
- # We prevent pybids from crashing the fmriprep run when it can't read those, by
- # wiping them out temporarily via renaming.
- # We spare only those that belong to the participant we want to process.
- # After job completion, the jsons will be restored.
- # See https://github.com/bids-standard/pybids/issues/631 for more information.
- find inputs/data -mindepth 2 -name '*.json' -a ! -wholename "$subid" | sed -e "p;s/json/xyz/" | xargs -n2 mv
- # execute fmriprep. Its runscript is available as /singularity within the
- # container. Custom fmriprep parametrization can be done here.
- /singularity inputs/data . participant --participant-label $subid \
- -w .git/tmp/wdir --skip-bids-validation \
- --use-aroma --fs-license-file code/license.txt
- # restore the jsons we have moved out of the way
- find inputs/data -mindepth 2 -name '*.xyz' -a ! -wholename "$subid" | sed -e "p;s/xyz/json/" | xargs -n2 mv
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