fmriprep-all.sh

#!/usr/bin/env bash

# User inputs:
# sub='01 06 11 16'
# ds_name=auditory_vs_visual
# ds_nr=ds003717

sub=$1
ds_name=$2 
ds_nr=$3     
# Datapaths
rawdata_dir="/LOCAL/jzerbe/$ds_name/$ds_nr"
derivatives_dir="/LOCAL/jzerbe/$ds_name/$ds_nr/derivatives/fmriprep"
license_dir="/home/jzerbe/freesurfer.txt"
working_dir="/LOCAL/jzerbe/temp_working_dir_$ds_name"
memory=100000
cpus='30'

STARTTIME=$(date +%s)

# Loop through subjects string
for val in $sub; do
    if [ ! -d $working_dir ] 
    then
        mkdir $working_dir
    fi
    if [ ! -d $derivatives_dir ] 
    then
        mkdir $derivatives_dir
    fi
    # Run fmriprep:
    fmriprep-docker $rawdata_dir $derivatives_dir \
      participant \
      --participant-label $val \
      --skip-bids-validation \
      --fs-license-file $license_dir \
      --output-spaces T1w MNI152NLin2009cAsym MNI152NLin6Asym \
      --user 1022:1023 \
      --use-aroma \
      --error-on-aroma-warnings \
      --mem-mb $memory \
      --n_cpus $cpus \
      --work-dir $working_dir;

    rm -rf $working_dir;
done

#rm -rf $working_dir;

ENDTIME=$(date +%s)
echo "Duration in seconds: $(($ENDTIME - $STARTTIME))"