run_freesurfer_bids_7.2

#!/bin/bash

: '
Script to run recon-all for a subject dataset in bids format
Intended to be used with regularBatch with regularBatch, regularSubmit,
or in a regularInteractive job.

Originally form https://github.com/khanlab/neuroglia-helpers
Modified by: Ali Tafakkor, atafakko@uwo.ca 
'

# freeSurfer version to load
version=7.2.0

# Print usage guide in case of missing passed arguments 
if [ "$#" -lt 2 ]
then 
 echo "Freesurfer ${version} *mini* bids-app  - runs recon-all -parallel -hires -threads 8 -all ... "
 echo ""
 echo "Must use this command with regularBatch, regularSubmit, or in a regularInteractive job"
 echo " as it uses the SLURM_TMPDIR local scratch to run. "
 echo ""
 echo "Usage: $0 <subject> <bids_dir> <output_dir> <optional recon-all args>"
 echo ""
 echo " e.g.: regularBatch $0 subjects.txt -a "\"/path/to/bids_dir /path/to/output_dir\"" -j 8core32gb12h "
 echo " where each line of subjects.txt contains e.g. sub-001"
 exit 1
fi

# first passed argument would be the subject id
subject=$1

# take the input bids and output directories 
# as the second arguments divided by a space
bids_dir=`realpath $(echo "$2" | awk '{print $1}')`
out_dir=`realpath $(echo "$2" | awk '{print $2}')`

# Make sure the script is running on a compute node
if [ -z "$SLURM_TMPDIR" ]; then echo "must run this script on compute node"; exit 1; else echo "SLURM_TMPDIR=$SLURM_TMPDIR"; fi

shift 2
optargs=$@

# Select the T1w or MP2RAGE anatomical scans assuming BIDS structure 
# You can modify to more narrowly filter files
in_imgs=`ls $bids_dir/${subject}/*/anat/*T1w.nii.gz $bids_dir/${subject}/anat/*MP2RAGE_T1map.nii.gz`

in_cmd=""
for img in $in_imgs
do
 in_cmd="$in_cmd -i $img"
done
    
# Load specified freesurfer version
module load freesurfer/${version}
# Create output directory
mkdir -p $out_dir

# Run recon-all in tempdir, then copy it over when finished
recon-all -threads 8 -sd $SLURM_TMPDIR  -subjid $subject -parallel -hires -all $in_cmd $optargs
if [ "$?" = "0" ]
then
    pushd $SLURM_TMPDIR
    tar -cvf $out_dir/$subject.tar ${subject} 
    popd
else
    touch $out_dir/$subject.FAILED
fi