generate_rmds

#! /bin/bash

TEMPLATEDIR=/mnt/home/natkoh/shinyQA
PROJECTDIR=/mnt/panuc/udallp2

usage()
{
    echo "Usage: `basename $0` <subject id> <session no> <task>"
    echo
    echo "<subject id> format must be numbers only: e.g. 100044 or 100054"
    echo
    echo "<session no> should be a single number: e.g. 1 or 2"
    echo
    echo "<task> should be either one of these: rest-on, rest-off, axcpt-on, axcpt-off"
    echo
}

if [ $# -lt 3 ]; then
	echo
	echo   "./generate_rmds <subject id> <session no> <task>"
	echo   "e.g. ./generate_rmds 100044 1 rest-on"
	echo
	exit
fi

SUBID=$1
NO=$2
TASK=$3

# parrec
if [ -f ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA/${TASK}_parrec.Rmd ]; then
    rm ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA/${TASK}_parrec.Rmd
fi
cp ${TEMPLATEDIR}/TASK_parrec.Rmd  ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA/${TASK}_parrec.Rmd
cd ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA
sed -i "s~PROJECTDIR~$PROJECTDIR~g" ${TASK}_parrec.Rmd 
sed -i "s/SUBID/$SUBID/g" ${TASK}_parrec.Rmd 
sed -i "s/NO/$NO/g" ${TASK}_parrec.Rmd 
sed -i "s/TASK/$TASK/g" ${TASK}_parrec.Rmd

# motion
if [ -f ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA/${TASK}_motion.Rmd ]; then
    rm ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA/${TASK}_motion.Rmd
fi
cp ${TEMPLATEDIR}/TASK_motion.Rmd  ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA/${TASK}_motion.Rmd
cd  ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA
sed -i "s~PROJECTDIR~$PROJECTDIR~g" ${TASK}_motion.Rmd 
sed -i "s/SUBID/$SUBID/g" ${TASK}_motion.Rmd 
sed -i "s/NO/$NO/g" ${TASK}_motion.Rmd 
sed -i "s/TASK/$TASK/g" ${TASK}_motion.Rmd

# warning
if [ -f ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA/${TASK}_warning.Rmd ]; then
    rm ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA/${TASK}_warning.Rmd
fi
cp ${TEMPLATEDIR}/TASK_warning.Rmd  ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA/${TASK}_warning.Rmd
cd  ${PROJECTDIR}/subjects/${SUBID}/session${NO}/QA
sed -i "s~PROJECTDIR~$PROJECTDIR~g" ${TASK}_warning.Rmd 
sed -i "s/SUBID/$SUBID/g" ${TASK}_warning.Rmd 
sed -i "s/NO/$NO/g" ${TASK}_warning.Rmd 
sed -i "s/TASK/$TASK/g" ${TASK}_warning.Rmd

# copy and rename parrecs

# generate numvols file for each task