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test.sh
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test.sh
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# conda activate mydatalad
# example usage:
# $ bash test.sh legacy # for legacy output layout
# $ bash test.sh bids # for BIDS output layout
output_layout=$1 # "legacy" or "bids" (default)
# ++++++++++++++++++++++ [FIX ME] ++++++++++++++++++++++++++
main_folder="/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/data"
input_dir="${main_folder}/t8urc" # single-ses toy data
output_main_dir="${main_folder}/test_fmriprepfake"
subid="sub-01"
# +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
output_dir=${output_main_dir}/"fmriprep-"${output_layout}"-layout"
# check if the output_dir exists:
if [[ -d ${output_dir} ]]; then
echo "test.sh: removing the existing output folder..."
rm -r ${output_dir}
fi
cmd="python fake_script.py"
cmd+=" ${input_dir}"
cmd+=" ${output_dir}"
cmd+=" participant"
cmd+=" --participant-label=${subid}"
if [[ $output_layout == "legacy" ]]; then
cmd+=" --output-layout ${output_layout}" # if it's "bids", no need to add.
fi
echo $cmd
$cmd