fmriprep_Scripted.sh

#!/bin/bash

subject=$1

  #User inputs:
  bids_root_dir=$HOME/Desktop/Flanker
  subj=$subject
  nthreads=4
  mem=20 #gb
  container=docker #docker or singularity

  #Begin:

  #Convert virtual memory from gb to mb
  mem=`echo "${mem//[!0-9]/}"` #remove gb at end
  mem_mb=`echo $(((mem*1000)-5000))` #reduce some memory for buffer space during pre-processing

  #export TEMPLATEFLOW_HOME=$HOME/.cache/templateflow
  export FS_LICENSE=$HOME/Desktop/Flanker/derivatives/license.txt

  #Run fmriprep
  if [ $container == singularity ]; then
    unset PYTHONPATH; singularity run -B $HOME/.cache/templateflow:/opt/templateflow $HOME/fmriprep.simg \
      $bids_root_dir $bids_root_dir/derivatives \
      participant \
      --participant-label $subj \
      --skip-bids-validation \
      --md-only-boilerplate \
      --fs-license-file $HOME/Desktop/Flanker/derivatives/license.txt \
      --fs-no-reconall \
      --output-spaces MNI152NLin2009cAsym:res-2 \
      --nthreads $nthreads \
      --stop-on-first-crash \
      --mem_mb $mem_mb \
      -w $HOME
  else
    fmriprep-docker $bids_root_dir $bids_root_dir/derivatives \
      participant \
      --participant-label $subj \
      --skip-bids-validation \
      --md-only-boilerplate \
      --fs-license-file $HOME/Desktop/Flanker/derivatives/license.txt \
      --fs-no-reconall \
      --output-spaces MNI152NLin2009cAsym:res-2 \
      --nthreads $nthreads \
      --stop-on-first-crash \
      --mem_mb $mem_mb \
      -w $HOME
  fi