makeROI_batch.sh

#!/bin/bash
# feed csv of ROI coordinates to make seeds
# run while in RestingState scripts directory
scriptPath=$(perl -e 'use Cwd "abs_path";print abs_path(shift)' "$0")
Path=$(dirname "$scriptPath")
echo "$Path"
cd "$Path" || exit

# example csv setup: net	x	y	z	diameter	seed	StudyOrigin
#                    DMN	6      -60	32	14	        rPCC	  UIUC

Usage() {
	echo "Usage: makeROI_batch.sh <csv file with list of ROIs, coordinates, size and study origin> <optional: define study origin if csv contains more than one study>"
	exit
}

[ "$1" = "" ] && Usage


inDir=$(dirname "${1}")
if [ -e "$inDir"/runseeds.txt ]; then
   rm "$inDir"/runseeds.txt
fi

tr '\015' '\012' < "${1}" > tmp_seedList.csv

awk -F, '{$1=$1"_"$x;for(i=1;i<=NF;i++)if(i!=x)f=f?f FS $i:$i;print f;f=""}' x=6 tmp_seedList.csv > tmp_seedList2.csv
mv tmp_seedList2.csv tmp_seedList.csv

awk -F","  'NR!=1{print $1}' tmp_seedList.csv | while IFS= read -r seed; do
    echo "$seed"
    coord=$(awk -v var="$seed" -F"," '{if($1==var) print $2,$3,$4;}' tmp_seedList.csv)

    if [[ $2 == "" ]]; then
        study=$(awk -v var="$seed" -F"," '{if($1==var) print $6;}' tmp_seedList.csv)
    else
        study=${2}
    fi

    size=$(awk -v var="$seed" -F"," '{if($1==var) print $5;}' tmp_seedList.csv)

    sh makeROI.sh "$coord" mm "$size" sphere "${study}_${seed}"


    # txt file of newly made seeds that can be fed into seedVoxelCorrelation.sh
    echo "${study}_${seed}" >> "$inDir"/runseeds.txt
done


#rm temporary files if necessary
if [ -e tmp_seedList.csv ]; then
   rm tmp_seedList.csv
fi