move2xnat

#!/bin/bash
function helpme()
{
echo "USAGE: move2xnat -datadir=<path_to_subjects> -studyname=<your_study_name>"
echo 
echo "This will move your dicoms and recon-all output to"
echo "xnat and replace the data current directories with "
echo "symlinks to the data :)"
echo
echo "Please ensure that <path_to_subjects> contains a"
echo "directory called dicoms as well as the recon-all"
echo "generated output directories"
echo
echo "Written by John Salvatore -- jsalva@mit.edu"
exit 0
}

function main()
{

xnatsurfdir="/mindhive/xnat/surfaces/${studyname}"
xnatdicomdir="/mindhive/xnat/dicom_storage/${studyname}"
for d in $(find ${datadir} -maxdepth 1 -type d |sed "s|${datadir}\/||g"); do 
	echo $d

	
	if [ ! -d "${xnatdicomdir}/$d" ];then
		cmd="mkdir -p ${xnatdicomdir}/$d"
		echo ${cmd}
		eval ${cmd}
	fi
	if [ ! -d "${xnatsurfdir}/$d" ];then
		cmd="mkdir -p ${xnatsurfdir}/$d"
		echo ${cmd}
		eval ${cmd}
	fi


	#echo "rsync -rLptgD /mindhive/gablab/CARD/data/$d/dicoms ${xnatdir}/$d" | qsub -V -q bigmem
	dicomdir="${datadir}/$d/dicoms"
	echo ${dicomdir}
	if [ ! -L ${dicomdir} ]; then
		mv ${dicomdir} ${xnatdicomdir}/$d
		ln -s "${xnatdicomdir}/$d/dicoms" "${dicomdir}"
	fi
	
	for dir in surf mri label bem src "touch" scripts stats tmp trash; do


		fsdir=${datadir}/$d/${dir}
		echo ${fsdir}
		if [ ! -L ${fsdir} ]; then
			mv ${fsdir} ${xnatsurfdir}/$d
			ln -s ${xnatsurfdir}/$d/${dir} ${fsdir}
		fi

	done
	
	

done
exit 1
}

if [ $# != 0 ]; then

	for arg in "$@"
	do
		case "${arg}" in
			-h|-help|help) 
			helpme
			;;
			-datadir=*|-data=*)
			darg=`echo ${arg} | sed 's/[-a-zA-Z0-9]*=//'`
			echo "darg = "$darg
			datadir=${darg}
			;;
			-studyname=*|-study=*)
			sarg=`echo ${arg} | sed 's/[-a-zA-Z0-9]*=//'`
			studyname=${sarg}
			echo "sarg = "$sarg
			;;
			*)
			echo "Error: Nonsense input, aborting"
			exit 0
			;;
		esac
	
	
		
	done	
	main	
fi

echo "Error: No arguments. Try again with -help"
exit 0