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bedpostx
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bedpostx
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#!/bin/sh
# Copyright (C) 2004,2013 University of Oxford
#
# Part of FSL - FMRIB's Software Library
# http://www.fmrib.ox.ac.uk/fsl
# fsl@fmrib.ox.ac.uk
#
# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
# Imaging of the Brain), Department of Clinical Neurology, Oxford
# University, Oxford, UK
#
#
# LICENCE
#
# FMRIB Software Library, Release 5.0 (c) 2012, The University of
# Oxford (the "Software")
#
# The Software remains the property of the University of Oxford ("the
# University").
#
# The Software is distributed "AS IS" under this Licence solely for
# non-commercial use in the hope that it will be useful, but in order
# that the University as a charitable foundation protects its assets for
# the benefit of its educational and research purposes, the University
# makes clear that no condition is made or to be implied, nor is any
# warranty given or to be implied, as to the accuracy of the Software,
# or that it will be suitable for any particular purpose or for use
# under any specific conditions. Furthermore, the University disclaims
# all responsibility for the use which is made of the Software. It
# further disclaims any liability for the outcomes arising from using
# the Software.
#
# The Licensee agrees to indemnify the University and hold the
# University harmless from and against any and all claims, damages and
# liabilities asserted by third parties (including claims for
# negligence) which arise directly or indirectly from the use of the
# Software or the sale of any products based on the Software.
#
# No part of the Software may be reproduced, modified, transmitted or
# transferred in any form or by any means, electronic or mechanical,
# without the express permission of the University. The permission of
# the University is not required if the said reproduction, modification,
# transmission or transference is done without financial return, the
# conditions of this Licence are imposed upon the receiver of the
# product, and all original and amended source code is included in any
# transmitted product. You may be held legally responsible for any
# copyright infringement that is caused or encouraged by your failure to
# abide by these terms and conditions.
#
# You are not permitted under this Licence to use this Software
# commercially. Use for which any financial return is received shall be
# defined as commercial use, and includes (1) integration of all or part
# of the source code or the Software into a product for sale or license
# by or on behalf of Licensee to third parties or (2) use of the
# Software or any derivative of it for research with the final aim of
# developing software products for sale or license to a third party or
# (3) use of the Software or any derivative of it for research with the
# final aim of developing non-software products for sale or license to a
# third party, or (4) use of the Software to provide any service to an
# external organisation for which payment is received. If you are
# interested in using the Software commercially, please contact Isis
# Innovation Limited ("Isis"), the technology transfer company of the
# University, to negotiate a licence. Contact details are:
# innovation@isis.ox.ac.uk quoting reference DE/9564.
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