bedpostX

#!/bin/sh

#   Copyright (C) 2004 University of Oxford
#
#   SHCOPYRIGHT

if [ "x$SGE_ROOT" = "x" ] ; then
  . /usr/local/share/sge-6.0/default/common/settings.sh
fi

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
}

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

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"
fi

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

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

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

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

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

echo Making bedpost directory structure

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

mailto=`whoami`@fmrib.ox.ac.uk

echo Queuing preprocessing stages
preprocid=`qsub -M $mailto -V -q short.q \
    -o ${subjdir}.bedpost/logs -e ${subjdir}.bedpost/logs \
    ${FSLDIR}/bin/bedpostX_preproc.sh ${subjdir} | \
    awk '{print $3}'`

echo Queuing parallel processing stage
nslices=`avwval ${subjdir}/data dim3`
bedpostid=`qsub -M $mailto -hold_jid $preprocid -V -q long.q -t 1-$nslices \
    -o ${subjdir}.bedpost/logs -e ${subjdir}.bedpost/logs \
    ${FSLDIR}/bin/bedpostX_single_slice.sh $subjdir | \
    awk '{print $3}' | awk -F. '{print $1}'`

echo Queuing post processing stage
mergeid=`qsub -M $mailto -hold_jid $bedpostid -V -q short.q \
    -o ${subjdir}.bedpost/logs -e ${subjdir}.bedpost/logs \
    ${FSLDIR}/bin/bedpostX_postproc.sh $subjdir | \
    awk '{print $3}'`

echo
echo Type ${subjdir}.bedpost/monitor to show progress.
cat <<EOM > ${subjdir}.bedpost/monitor
#!/bin/sh
finished=0
logdir=${subjdir}.bedpost/logs
while [ \$finished -eq 0 ] ; do
    nfin=0
    if [ -f \$logdir/bedpost.o$bedpostid.1 ] ; then
      nfin=\`cat \$logdir/bedpost.o$bedpostid.* |\
        grep Done | wc -w | awk '{print \$1}'\` 
    fi
    if [ \$nfin -eq $nslices ] ; then
        finished=1
    fi

    echo "\$nfin slices processed"
    sleep 600;
done
EOM
chmod +x ${subjdir}.bedpost/monitor

echo Type ${subjdir}.bedpost/cancel to terminate the task.
cat <<EOC > ${subjdir}.bedpost/cancel
#!/bin/sh
qdel $mergeid $bedpostid $preprocid
EOC
chmod +x ${subjdir}.bedpost/cancel

echo
echo You will get an email at the end of the post-processing stage.
echo