bedpostx

#!/bin/sh

#   Copyright (C) 2004,2013 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
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#   Imaging of the Brain), Department of Clinical Neurology, Oxford
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#   Oxford (the "Software")
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FSL_SUB=/usr/share/fsl/overlay/fsl_sub
export LC_ALL=C

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 "expects to find grad_dev in subject directory, if -g is set"
    echo "options (old syntax)"
    echo "-n (number of fibres per voxel, default 2)"
    echo "-w (ARD weight, more weight means less secondary fibres per voxel, default 1)"
    echo "-b (burnin period, default 1000)"
    echo "-j (number of jumps, default 1250)"
    echo "-s (sample every, default 25)"
    echo "-model (1 for monoexponential, 2 for multiexponential, default 1)"
    echo "-g (consider gradient nonlinearities, default off)"
    echo "-c do not use CUDA capable hardware/queue (if found)"
    echo ""
    echo ""
    echo "ALTERNATIVELY: you can pass on xfibres options onto directly bedpostx"
    echo " For example:  bedpostx <subject directory> --noard --cnonlinear"
    echo " Type 'xfibres --help' for a list of available options "
    echo " Default options will be bedpostx default (see above), and not xfibres default."
    echo ""
    echo "Note: Use EITHER old OR new syntax."
    exit 1
}

monitor(){
    cat <<EOM > ${subjdir}.bedpostX/monitor
#!/bin/sh
echo
echo "----- Bedpostx Monitor -----"
finished=0
lastprinted=0
havedad=2
while [ \$finished -eq 0 ] ; do
    nfin=0
    slice=0
    errorFiles=\`ls ${subjdir}.bedpostX/logs/*.e* 2> /dev/null \`
    for errorFile in \$errorFiles
    do
        if [ -s \$errorFile ]; then
            echo An error ocurred. Please check file \$errorFile
            kill -9 $$
            exit 1
        fi
    done
    while [ \$slice -le $nslices ];do
        if [ -e ${subjdir}.bedpostX/logs/monitor/\$slice ]; then
            nfin=\$((\$nfin + 1))
        fi
        slice=\$((\$slice + 1))
    done
    newmessages=\$((\$nfin - \$lastprinted))
    while [ "\$newmessages" -gt 0 ];do
        lastprinted=\$((\$lastprinted + 1))
        echo \$lastprinted slices processed out of $nslices
        newmessages=\$((\$newmessages - 1))
    done
    if [ -f ${subjdir}.bedpostX/xfms/eye.mat ] ; then
        finished=1
        echo "All slices processed"
	exit 
    fi
    if [ ! \$havedad -gt 0 ]; then
       exit 0
    fi
    if [ "x$SGE_ROOT" = "x" ]; then
        havedad=\`ps -e -o pid | grep "$$\\b" | wc -l\`        
    fi
    sleep 180;
done
EOM
    chmod +x ${subjdir}.bedpostX/monitor
}

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

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

#parse option arguments
nfibres=2
fudge=1
burnin=1000
njumps=1250
sampleevery=25
model=1
gflag=0
nocuda=0
other=""

shift
while [ ! -z "$1" ]
do
  case "$1" in
      -n) nfibres=$2;shift;;
      -w) fudge=$2;shift;;
      -b) burnin=$2;shift;;
      -j) njumps=$2;shift;;
      -s) sampleevery=$2;shift;;
      -model) model=$2;shift;;
      -g) gflag=1;;
      -c) nocuda=1;;
      *) other=$other" "$1;;
  esac
  shift
done
opts="--nf=$nfibres --fudge=$fudge --bi=$burnin --nj=$njumps --se=$sampleevery --model=$model"
defopts="--cnonlinear"
opts="$opts $defopts $other"
if [ -n "$SGE_ROOT" ]; then
	# Look for an SGE queue
	if [ -n $FSLGECUDAQ -a $nocuda -eq 0 ]; then
		# Test that the queue exists
		qconf -sq $FSLGECUDAQ 2>&1 >/dev/null
		if [ $? -eq 0 ]; then
			# CUDA queue exists
			if [ -x $0_gpu ]; then
				exec $0_gpu $myopts
			fi
		fi
	fi
fi

echo subjectdir is $subjdir

#check that all required files exist

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

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

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

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

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

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

if [ -e ${subjdir}.bedpostX/xfms/eye.mat ]; then
	echo "${subjdir} has already been processed: ${subjdir}.bedpostX." 
	echo "Delete or rename ${subjdir}.bedpostX before repeating the process."
	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/monitor
mkdir -p ${subjdir}.bedpostX/xfms

# This setting is already present in fsl_sub and allows for a more flexible,
# centralized configuration
#mailto=`whoami`@fmrib.ox.ac.uk
echo Queuing preprocessing stages
# don't setup email options, rely on fsl_sub's setting
#preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}`
#preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}`
preprocid=$( ${FSL_SUB} -T 60 -N bpx_preproc -l ${subjdir}.bedpostX/logs -B ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}  )

echo Queuing parallel processing stage
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt

monitor
# Don't be SGE-specific -- rely on FSLPARALLEL
if [ "x$FSLPARALLEL" = "x" ]; then
    ${subjdir}.bedpostX/monitor&
fi

slice=0
while [ $slice -lt $nslices ]
do
    slicezp=`$FSLDIR/bin/zeropad $slice 4`
    if [ `$FSLDIR/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_$slicezp/dyads1` -eq 1 ] && [ -f ${subjdir}.bedpostX/logs/monitor/$slice ];then
	echo "slice $slice has already been processed"
    else
        [ -f ${subjdir}.bedpostX/logs/monitor/$slice ] && rm ${subjdir}.bedpostX/logs/monitor/$slice
	if [ ${gflag} -eq 1 ]; then
	    gopts="$opts --gradnonlin=${subjdir}/grad_dev_slice_${slicezp}"
	else
	    gopts=$opts
	fi    
	echo "${FSLDIR}/bin/bedpostx_single_slice.sh ${subjdir} ${slice} $gopts" \
	    >> ${subjdir}.bedpostX/commands.txt
    fi
    slice=$(($slice + 1))
done
# don't specify a mailto address, but rely on fsl_sub doing it
#bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
#bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
bedpostid=$( ${FSL_SUB} -l ${subjdir}.bedpostX/logs -N bedpostx -t ${subjdir}.bedpostX/commands.txt -B )

echo Queuing post processing stage
# don't setup email options, rely on fsl_sub's setting
#mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
#mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
mergeid=$(${FSL_SUB} -T 60 -N bpx_postproc -l ${subjdir}.bedpostX/logs -B ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir)

# Don't be SGE-specific -- rely on FSLPARALLEL
if [ "x$FSLPARALLEL" != "x" ]; then
    echo
    echo Type ${subjdir}.bedpostX/monitor to show progress.
    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
else
    sleep 190
fi