get some columns from fmriPrep's output using bash script

extract_cols_from_tsv.sh

#!/bin/bash

# columns to extract
colterms="csf white_matter global_signal trans_x trans_y trans_z rot_x rot_y rot_z"

printcol()
{
    local FILE=${1}
    local COLUMNTITLE=${2} 

    # check if even there
    local ccc=$(head -1 $FILE | grep $COLUMNTITLE)
    if [[ -z $ccc ]] ; then
    	>&2 echo "$ccc not in file. error." 
    	rm -v $tmp_file_1
		rm -v $tmp_file_2
		rm -v $tmp_file_3 
    	exit 1
    fi

    cut $FILE -f `head -1 $FILE | tr "\t" "\n" | grep -n "^$COLUMNTITLE"'$' | cut -f 1 -d :`
}

inputfile=$1
outfile=$2
cols=$3
if [[ -z $outfile ]] || [[ -z $inputfile ]] ; then
	echo "USAGE: $0 inputfile outputfile [optional string of columns to extract, use quote around whole string]"
	exit 1
fi

if [[ -e $outfile ]] ; then
	echo "$outfile already exists. please delete"
	exit 1
fi

if [[ ! -z $cols ]] ; then
	colterms=$cols
fi

################################################################################

tmp_file_1=$(mktemp /tmp/getcols.XXXXXX)
tmp_file_2=$(mktemp /tmp/getcols.XXXXXX)
tmp_file_3=$(mktemp /tmp/getcols.XXXXXX)

> $tmp_file_1
for CC in $colterms ; do

	printcol $inputfile $CC > ${tmp_file_2}
	if [[ -s ${tmp_file_1} ]] ; then
		paste -d',' ${tmp_file_1} ${tmp_file_2} > ${tmp_file_3}
		mv $tmp_file_3 $tmp_file_1
	else
		mv $tmp_file_2 $tmp_file_1
	fi

done

mv $tmp_file_1 $outfile
#rm -v $tmp_file_1
rm -v $tmp_file_2
#rm -v $tmp_file_3

Hi! Thanks for this script! I just want to how to use it? Is it a function with 3 input? what exactly shoud they be?

Thanks!