old_bedpost

#!/bin/sh

Usage() {
    echo ""
    echo "Usage: bedpost <subject directory> "
    echo ""
    echo "expects to find bvals and bvecs in subject directory"
    echo "expects to find data nodif_brain_mask nodif in subject directory"
    echo ""
    exit
}

trap Clean_Exit 2


Clean_Exit(){

	if [ -d ${subjdir}.bedpost/logs/pid_${$} ];then
	    i=`ls  ${subjdir}.bedpost/logs/pid_${$}`
	    for j in ${i};do 
		host=`echo $j | awk -F _fdt_ '{print $1}'`
		pid=`echo $j | awk -F _fdt_ '{print $2}'`
		if [ "x${FSLMACHINELIST}" != "x" ]; then
#	            ${FSLREMOTECALL} $host "kill -KILL $pid" #this leaves one child process per processor - what can you do?
		 echo "if [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_kill_pid ${pid} >/dev/null 2>&1; else echo FSLDIR not set in any default location on machine `hostname`;fi" | $FSLREMOTECALL $host /bin/sh >/dev/null 2>&1 &
		else
		    ${FSLDIR}/bin/bedpost_kill_pid ${pid}
		fi
		rm ${subjdir}.bedpost/logs/pid_${$}/${j}
	    done
	fi
	ExitUnlock;
}

Lock(){
    if [ "x${FSLLOCKDIR}" != "x" ];then
	touch ${FSLLOCKDIR}/.bedpost.lock
    fi
}

ExitUnlock(){
    if [ -e ${FSLLOCKDIR}/.bedpost.lock ];then
	rm ${FSLLOCKDIR}/.bedpost.lock
    fi

    #clean up slices
    ndat_sl=`echo ${subjdir}/data_slice_* | grep -v "slice_\*" |wc -w` 
    nnodif_sl=`echo ${subjdir}/nodif_brain_mask_slice_* | grep -v "slice_\*" |wc -w` 
    if [ $ndat_sl -ge 0 ] ;then 
	rm -f ${subjdir}/data_slice_*
    fi
    
    if [ $nnodif_sl -ge 0 ] ;then 
	rm -f ${subjdir}/nodif_brain_mask_slice_*
    fi
    
    exit
}

LockTest(){
    if [ "x${FSLLOCKDIR}" = "x" ];then
	echo 1;
    elif [ ! -e ${FSLLOCKDIR}/.bedpost.lock ];then
	echo 1;
    else
	echo 0;
    fi
}

make_absolute(){
    dir=$1;
    if [ -d ${dir} ]; then
	OLDWD=`pwd`
	cd ${dir}
	dir_all=`pwd`
	cd $OLDWD
    else
	dir_all=${dir}
    fi
    echo ${dir_all}
}



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

if [ `LockTest` -eq 0 ]; then
    echo "bedpost is currently being run - try again later"
    exit
fi

if [ "x${FSLMACHINELIST}" != "x" ];then
    if [ "x${FSLREMOTECALL}" = "x" ];then
	echo "error: you must set FSLREMOTECALL if you have set FSLMACHINELIST"
	exit
    fi
fi

Lock;

subjdir=`make_absolute $1`
subjdir=`echo $subjdir | sed 's/\/$/$/g'`

echo subjectdir is $subjdir

#check that all required files exist

if [ ! -d $subjdir ]; then
	echo "subject directory $1 not found"
	ExitUnlock
fi

if [ ! -e ${subjdir}/bvecs ]; then
	echo "${subjdir}/bvecs not found"
	ExitUnlock
fi

if [ ! -e ${subjdir}/bvals ]; then
	echo "${subjdir}/bvals not found"
	ExitUnlock
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
	echo "${subjdir}/data not found"
	ExitUnlock
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` -eq 0 ]; then
	echo "${subjdir}/nodif not found"
	ExitUnlock
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
	echo "${subjdir}/nodif_brain_mask not found"
	ExitUnlock
fi


echo making bedpost directory
mkdir -p ${subjdir}.bedpost/
mkdir -p ${subjdir}.bedpost/diff_slices

echo copying files to bedpost directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpost
${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpost
${FSLDIR}/bin/avwmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpost/nodif_brain


mkdir -p ${subjdir}.bedpost/logs
mkdir -p ${subjdir}.bedpost/logs/pid_${$}

nslices=`avwval ${subjdir}/data dim3`

${FSLDIR}/bin/avwslice ${subjdir}/data
${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask

#for parallel processing, the following need to be setup elsewhere
#FSLMACHINELIST="list of machines (can be duplicated for two processors etc.)"
#FSLREMOTECALL="ssh (or rsh or whatever you want to use)"

if [ "x$FSLMACHINELIST" = "x" ] ; then
    echo "processing data on local host"
    ${FSLDIR}/bin/bedpost_proc $subjdir $nslices ${subjdir}.bedpost/logs/pid_${$} &
else
    echo "processing data on hosts: $FSLMACHINELIST"
    for machine in $FSLMACHINELIST; do
	echo "if [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_proc $subjdir $nslices ${subjdir}.bedpost/logs/pid_${$}; else echo FSLDIR not set in any default location on machine `hostname`;fi"|	$FSLREMOTECALL $machine /bin/sh  &
    done
fi


b=0
finished=0;
while [ $finished -eq 0 ];do
    b=`expr $b + 1 `
    sleep 60;
    nfin=`echo ${subjdir}.bedpost/logs/.*_finished | grep -v ".\*" |wc -w` 
    if [ $nfin -eq $nslices ];then
	finished=1;
    fi
    if [ $b -eq 10 ]; then 
	echo "$nfin slices processed"
	b=0
    fi	
done

#postprocessing
#postprocess $subjdir

##this will have to change..
echo "Merging outputs into 4D files"

${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_fsamples  `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/f_samples`
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_thsamples -Tmean ${subjdir}.bedpost/mean_thsamples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_phsamples -Tmean ${subjdir}.bedpost/mean_phsamples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_fsamples -Tmean ${subjdir}.bedpost/mean_fsamples

if [ ${finished} -eq 1 ];then
    if [ `imtest ${subjdir}.bedpost/merged_thsamples` -eq 1 ];then
	if [ `imtest ${subjdir}.bedpost/merged_phsamples` -eq 1 ];then
	    if [ `imtest ${subjdir}.bedpost/merged_fsamples` -eq 1 ];then
		rm -rf ${subjdir}.bedpost/diff_slices
		rm -f ${subjdir}/data_slice_*
		rm -f ${subjdir}/nodif_brain_mask_slice_*
	    fi
	fi
    fi
fi



mkdir -p ${subjdir}.bedpost/xfms
xfmdir=${subjdir}.bedpost/xfms
echo 1 0 0 0 > ${xfmdir}/eye.mat
echo 0 1 0 0 >> ${xfmdir}/eye.mat
echo 0 0 1 0 >> ${xfmdir}/eye.mat
echo 0 0 0 1 >> ${xfmdir}/eye.mat

echo "DONE"
ExitUnlock()