subject_setup.sh

#!/bin/bash
#SBATCH --output=sub_setup_logs/%x_%j.out
#SBATCH --time=02-00:30:30
#SBATCH -n 1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=4G
#SBATCH --partition=ncf
#SBATCH --account=mclaughlin_lab
set -axo pipefail
set +eu

module load Anaconda3/2019.10 python/3.7.7-fasrc01
module load centos6/0.0.1-fasrc01  ncf/1.0.0-fasrc01 dcm2niix/2019_09_04-ncf freesurfer/6.0.0-ncf fsl/6.0.2-ncf

CBS_ID=$1
ID=`echo $CBS_ID | awk -F "_" '{print $3$4}'`
SUBJECT=`echo $CBS_ID | awk -F "_" '{print "sub-"$3$4}'`
STAR_DIR="/mnt/stressdevlab/STAR"
STAR_SUB_DIR="${STAR_DIR}/${SUBJECT}"
SOURCE_SUB_DIR="${STAR_DIR}/sourcedata/${SUBJECT}"

cat << EOF
    /**********************/
   /*                     /
  /* ${CBS_ID}
 /*---------------------/
/**********************/
EOF
echo "Downloading and processing data for $SUBJECT"

#Activate py37
source activate star

set -eu

#Get scans from CBSCentral
echo "Downloading data from CBSCentral..."
python ${STAR_DIR}/derivatives/yaxil_dl.py ${CBS_ID}

#Run commands outputted from yaxildl
echo "Running commands generated by yaxil_dl.py..."
pushd ${SOURCE_SUB_DIR}
source ${SUBJECT}_conv_cmds.txt
    
#Copy files to subject directory
echo "Copying files to ${STAR_SUB_DIR}..."
mkdir -p ${STAR_SUB_DIR}
for d in func dwi anat; do
    cp -r ${d}/ ${STAR_SUB_DIR}/
done

#Prep fmap files
echo "Prep fmap files..."
python ${STAR_DIR}/derivatives/prep_fmap.py ${SUBJECT}

#Move fmap files
echo "Moving fmap files..."
while read line ; do
    eval $line
done < ${STAR_SUB_DIR}/fmap_cmds.txt
   
popd

echo "Running scripts in OnsetScripts/"
for pyfile in `ls OnsetScripts/*py`; do
	echo "${pyfile} ${ID};"	
	python ${pyfile} ${ID}; 
done