Simple FAL Freesurfer Runner using dcmstack and ArcGet

recon_script.sh

#!/usr/bin/env bash

load_freesurfer 5.3.0-centos4
export SUBJECTS_DIR=/ncf/jwb/studies/FallyMGH/Analyses/fsrecon_v1
export L1SINK=/ncf/jwb/studies/FallyMGH/Analyses/fmriNipype_v1/data/level1sink/

batch1=(FAL001 FAL002 FAL004 FAL009 FAL009 FAL010)
batch2=(FAL010 FAL013 FAL014 FAL020 FAL021 FAL024 FAL025 FAL026 FAL029)

for subj in "${batch2[@]}"; do
  rawdir=RAW/${subj}
  ArcGet.py -a cbscentral -r "MEMPRAGE RMS" -s ${subj}_MR1 --new-structure -o ${rawdir}
  dcmstack ${rawdir} --file-ext '.IMA'

  imgargs=''
  for img in ${rawdir}/*.nii*; do
    imgargs=$imgargs" -i ${img}"
  done

  recon-all $imgargs -subjid ${subj}
  rm -r $rawdir

  sbatch -p ncf -N 1 -n 1 --mem 4000 -t 2-0:00 -o ${subj}_fs -p  --wrap "recon-all -all -subjid ${subj} -qcache"

done

rmdir RAW