bedpostx

#!/bin/sh

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

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

Usage() {
    echo ""
    echo "Usage: bedpostx <subject directory> [options]"
    echo ""
    echo "expects to find bvals and bvecs in subject directory"
    echo "expects to find data and nodif_brain_mask in subject directory"
    echo "options:"
    echo "-n (number of fibres per voxel, default 2)"
    echo "-w (ARD weight, more weight means less fibres killed per voxel, default 1)"
    echo "-b (burnin period, default 1000)"
    echo "-j (number of jumps, default 1250)"
    echo "-s (sample every, default 25)"
    echo ""
    exit 1
}

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

#parse option arguments
nfibres=2
fudge=1
burnin=1000
njumps=1250
sampleevery=25
while [ ! -z "$2" ]
do
  case "$2" in
      -n) nfibres=$3;shift;;
      -w) fudge=$3;shift;;
      -b) burnin=$3;shift;;
      -j) njumps=$3;shift;;
      -s) sampleevery=$3;shift;;
      *) break;;
  esac
  shift
done

#check that all required files exist

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

if [ ! -e ${subjdir}/bvecs ]; then
	echo "${subjdir}/bvecs not found"
	exit 1
fi

if [ ! -e ${subjdir}/bvals ]; then
	echo "${subjdir}/bvals not found"
	exit 1
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
	echo "${subjdir}/data not found"
	exit 1
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
	echo "${subjdir}/nodif_brain_mask not found"
	exit 1
fi

echo Making bedpostx directory structure

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

mailto=`whoami`@fmrib.ox.ac.uk
echo Queuing preprocessing stages
preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}`

echo Queuing parallel processing stage
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
if [ "x$SGE_ROOT" = "x" ]; then
# 
# Need to set off a backgrounded monitoring task
# 
    cat <<EOM > ${subjdir}.bedpostX/monitor
#!/bin/sh
finished=0
logdir=${subjdir}.bedpostX/logs
while [ \$finished -eq 0 ] ; do
    nfin=0
    if [ -f \$logdir/bedpostx.o*.1 ] ; then
      nfin=\`cat \$logdir/bedpostx.o* |\
        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}.bedpostX/monitor
    ${subjdir}.bedpostX/monitor&
    monitorpid=$!
fi
slice=0
while [ $slice -lt $nslices ]
do
    echo "${FSLDIR}/bin/bedpostx_single_slice.sh $subjdir $nfibres $fudge $burnin $njumps $sampleevery $slice" \
	>> ${subjdir}.bedpostX/commands.txt
    slice=$(($slice + 1))
done
bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
[ "x$SGE_ROOT" = "x" ] && kill $monitorpid

echo Queuing post processing stage
mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`

if [ "x$SGE_ROOT" != "x" ]; then
    echo
    echo Type ${subjdir}.bedpostX/monitor to show progress.
    cat <<EOM > ${subjdir}.bedpostX/monitor
#!/bin/sh
finished=0
logdir=${subjdir}.bedpostX/logs
while [ \$finished -eq 0 ] ; do
    nfin=0
    if [ -f \$logdir/bedpostx.o$bedpostid.1 ] ; then
      nfin=\`cat \$logdir/bedpostx.o$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}.bedpostX/monitor

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

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