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Commit 3a276a09 authored by Tim Behrens's avatar Tim Behrens
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added bedpost scripts.

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Makefile
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...@@ -2,6 +2,6 @@ include ${FSLCONFDIR}/default.mk ...@@ -2,6 +2,6 @@ include ${FSLCONFDIR}/default.mk
PROJNAME = misc_scripts PROJNAME = misc_scripts
SCRIPTS = regscript remove_vols replacevols replace_and_average_fmrib SCRIPTS = regscript remove_vols replacevols replace_and_average_fmrib bedpost bedpostX bedpostX_postproc.sh bedpostX_preproc.sh bedpostX_single_slice.sh bedpost_postproc.sh bedpost_preproc.sh bedpost_single_slice.sh linkbedpost
all: all:
bedpost 0 → 100755
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#!/bin/sh
# Copyright (C) 2004 University of Oxford
#
# SHCOPYRIGHT
if [ "x$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/bedpost_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/bedpost_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/bedpost_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 ${subjdir}.bedpost/cancel
echo
echo You will get an email at the end of the post-processing stage.
echo
bedpostX 0 → 100755
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View file @ 3a276a09
#!/bin/sh
# Copyright (C) 2004 University of Oxford
#
# SHCOPYRIGHT
if [ "x$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
bedpostX_postproc.sh 0 → 100755
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− 0
View file @ 3a276a09
#!/bin/sh
subjdir=$1
#$ -S /bin/sh
#$ -V
#$ -N bp_postproc
#$ -m ae
echo cock
\ No newline at end of file
bedpostX_preproc.sh 0 → 100755
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− 0
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#!/bin/sh
subjdir=$1
#$ -S /bin/sh
#$ -V
#$ -N bpx_preproc
#$ -m a
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
${FSLDIR}/bin/avwslice ${subjdir}/data
${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
echo Done
\ No newline at end of file
bedpostX_single_slice.sh 0 → 100755
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− 0
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#!/bin/sh
subjdir=$1
slice=`expr $SGE_TASK_ID - 1`
slicezp=`${FSLDIR}/bin/zeropad $slice 4`
#$ -cwd -q long.q
#$ -S /bin/sh
#$ -V -N bedpostX
#$ -l arch=tru64
#$ -m a
${FSLDIR}/bin/xfibres\
--data=$subjdir/data_slice_$slicezp\
--mask=$subjdir/nodif_brain_mask_slice_$slicezp\
-b $subjdir/bvals -r $subjdir/bvecs\
--forcedir --logdir=$subjdir.bedpost/diff_slices/data_slice_$slicezp\
--nj=1000 --bi=600 --se=20 --upe=24 --nfibres=3 > $subjdir.bedpost/logs/log$slicezp && echo Done
bedpost_postproc.sh 0 → 100644
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− 0
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#!/bin/sh
subjdir=$1
#$ -S /bin/sh
#$ -V
#$ -N bp_postproc
#$ -m ae
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
${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpost/merged_thsamples ${subjdir}.bedpost/merged_phsamples ${subjdir}.bedpost/nodif_brain_mask ${subjdir}.bedpost/dyadic_vectors
echo Removing intermediate files
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 ${subjdir}/nodif_brain_mask_slice_*
fi
fi
fi
echo Creating identity xfm
xfmdir=${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
\ No newline at end of file
bedpost_preproc.sh 0 → 100644
+ 20
− 0
View file @ 3a276a09
#!/bin/sh
subjdir=$1
#$ -S /bin/sh
#$ -V
#$ -N bp_preproc
#$ -m a
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
${FSLDIR}/bin/avwslice ${subjdir}/data
${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
echo Done
\ No newline at end of file
bedpost_single_slice.sh 0 → 100755
+ 18
− 0
View file @ 3a276a09
#!/bin/sh
subjdir=$1
slice=`expr $SGE_TASK_ID - 1`
slicezp=`${FSLDIR}/bin/zeropad $slice 4`
#$ -cwd -q long.q
#$ -S /bin/sh
#$ -V -N bedpost
#$ -l arch=tru64
#$ -m a
${FSLDIR}/bin/diff_pvm\
--data=$subjdir/data_slice_$slicezp\
--mask=$subjdir/nodif_brain_mask_slice_$slicezp\
-b $subjdir/bvals -r $subjdir/bvecs\
--forcedir --logdir=$subjdir.bedpost/diff_slices/data_slice_$slicezp\
--nj=1300 --bi=300 --se=20 > $subjdir.bedpost/logs/log$slicezp && echo Done
linkbedpost 0 → 100755
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− 0
View file @ 3a276a09
#!/bin/sh
if [ $# -lt 1 ];then
echo "Usage: linkbedpost <sourcedir>"
echo ""
echo "linkbedpost /usr/people/dtiuser/OCMR/CONTROLS/2mmdata/OCMR_20_001.bedpost"
exit
fi
source=$1;
targ=`basename $1`
mkdir $targ
mkdir ${targ}/xfms
for i in `imglob ${source}/dti_* ${source}/mean_* ${source}/merged_* ${source}/dyad* ${source}/nodif_* ${source}/nodif_* ${source}/struct* ${source}/standard*`; do
j=`basename $i`;
ln -s $i ${targ}/$j
done
for i in ${source}/xfms/*.mat;do
j=`basename $i`;
ln -s $i ${targ}/xfms/${j}
done
for i in ${source}/bv*;do
j=`basename $i`;
ln -s $i ${targ}/$j
done
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