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Add option to use custom .bidsignore #35

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merged 1 commit into from
Nov 8, 2022
Merged

Add option to use custom .bidsignore #35

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16 changes: 12 additions & 4 deletions tar2bids
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,8 @@ function usage {
echo " -o <output_dir> : default=$output_dir"
echo " -N <num parallel cores> : default=0 (max cores)"
echo " -h <heuristic.py> : default=$heuristic"
echo " -w <tempdir> (--tempdir in heudiconv)"
echo " -w <tempdir> (--tempdir in heudiconv)"
echo " -b <bidsignore> : default=$execpath/etc/bidsignore"
echo " -O \"<additional heudiconv options>\" : default=$heudi_opts"
echo " -C : copy tarfiles to BIDS sourcedata folder"
echo " -D : enable defacing of T1w images : default will not deface"
Expand Down Expand Up @@ -49,7 +50,7 @@ do_dcm2niix=0
uniden_factor=6


while getopts "N:o:h:O:P:T:w:CDxU:" options; do
while getopts "N:o:h:O:P:T:w:b:CDxU:" options; do
case $options in
N ) echo " Overriding number of cores: $OPTARG" >&2
ncores=$OPTARG;;
Expand All @@ -67,6 +68,8 @@ while getopts "N:o:h:O:P:T:w:CDxU:" options; do
tarfile_search="$OPTARG";;
w ) echo " Using --tempdir=$OPTARG" >&2
tempdir=$OPTARG;;
b ) echo " Using custom .bidsignore: $OPTARG" >&2
bidsignore="$OPTARG";;
C ) echo " Copying source tarfiles to sourcedata" >&2
copytar=1;;
x ) echo " Running dcm2niix with no heuristics" >&2
Expand Down Expand Up @@ -469,8 +472,13 @@ do
grep -v CogAtlasID $json > $json.new && mv -v $json.new $json
done

echo " Adding default .bidsignore file..."
cp -v $execpath/etc/bidsignore $output_dir/.bidsignore
if [[ -n "$bidsignore" ]]; then
echo " Adding custom .bidsignore file..."
cp -v "$bidsignore" "$output_dir/.bidsignore"
else
echo " Adding default .bidsignore file..."
cp -v $execpath/etc/bidsignore $output_dir/.bidsignore
fi

echo " Removing _ROI#.nii.gz files (unused scale bars from qMRI)..."
rm -vf $output_dir/sub*/*/*ROI[0-9].nii.gz $output_dir/sub*/ses*/*ROI[0-9].nii.gz 2> /dev/null
Expand Down