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Commit 494227da authored by FSL Automated Build Engineer's avatar FSL Automated Build Engineer
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Removed old bedpost

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old_bedpostX deleted 100644 → 0
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View file @ 4eb3c4ae
#!/bin/sh
# SHCOPYRIGHT
if [ "x$SGE_ROOT" != "x" ] && [ -f $FSLDIR/bin/sge_bedpostX ] ; then
exec $FSLDIR/bin/sge_bedpostX $@
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 nodif_brain_mask nodif 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 ""
exit
}
trap Clean_Exit 2
Clean_Exit(){
if [ -d ${subjdir}.bedpostX/logs/pid_${$} ];then
i=`ls ${subjdir}.bedpostX/logs/pid_${$}`
for j in ${i};do
host=`echo $j | awk -F _fdt_ '{print $1}'`
pid=`echo $j | awk -F _fdt_ '{print $2}'`
if [ "x${FSLMACHINELIST}" != "x" ]; then
# ${FSLREMOTECALL} $host "kill -KILL $pid" #this leaves one child process per processor - what can you do?
echo "if [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpostX_kill_pid ${pid} >/dev/null 2>&1; else echo FSLDIR not set in any default location on machine `hostname`;fi" | $FSLREMOTECALL $host /bin/sh >/dev/null 2>&1 &
else
${FSLDIR}/bin/bedpostX_kill_pid ${pid}
fi
rm ${subjdir}.bedpostX/logs/pid_${$}/${j}
done
fi
ExitUnlock;
}
Lock(){
if [ "x${FSLLOCKDIR}" != "x" ];then
touch ${FSLLOCKDIR}/.bedpostX.lock
fi
}
ExitUnlock(){
if [ -f ${FSLLOCKDIR}/.bedpostX.lock ];then
rm ${FSLLOCKDIR}/.bedpostX.lock
fi
#clean up slices
ndat_sl=`echo ${subjdir}/data_slice_* | grep -v "slice_\*" |wc -w`
nnodif_sl=`echo ${subjdir}/nodif_brain_mask_slice_* | grep -v "slice_\*" |wc -w`
if [ $ndat_sl -ge 0 ] ;then
rm -f ${subjdir}/data_slice_*
fi
if [ $nnodif_sl -ge 0 ] ;then
rm -f ${subjdir}/nodif_brain_mask_slice_*
fi
exit
}
LockTest(){
if [ "x${FSLLOCKDIR}" = "x" ];then
echo 1;
elif [ ! -f ${FSLLOCKDIR}/.bedpostX.lock ];then
echo 1;
else
echo 0;
fi
}
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}
}
[ "$1" = "" ] && Usage
if [ `LockTest` -eq 0 ]; then
echo "bedpostX is currently being run - try again later"
exit
fi
if [ "x${FSLMACHINELIST}" != "x" ];then
if [ "x${FSLREMOTECALL}" = "x" ];then
echo "error: you must set FSLREMOTECALL if you have set FSLMACHINELIST"
exit
fi
fi
Lock;
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"
ExitUnlock
fi
if [ ! -f ${subjdir}/bvecs ]; then
echo "${subjdir}/bvecs not found"
ExitUnlock
fi
if [ ! -f ${subjdir}/bvals ]; then
echo "${subjdir}/bvals not found"
ExitUnlock
fi
if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
echo "${subjdir}/data not found"
ExitUnlock
fi
if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` -eq 0 ]; then
echo "${subjdir}/nodif not found"
ExitUnlock
fi
if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
echo "${subjdir}/nodif_brain_mask not found"
ExitUnlock
fi
#parse option arguments
nfibres=2
fudge=1
burnin=1000
while [ ! -z "$2" ]
do
case "$2" in
-n) nfibres=$3;shift;;
-w) fudge=$3;shift;;
-b) burnin=$3;shift;;
*) break;;
esac
shift
done
echo making bedpostX directory
mkdir -p ${subjdir}.bedpostX/
mkdir -p ${subjdir}.bedpostX/diff_slices
echo copying files to bedpostX directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
mkdir -p ${subjdir}.bedpostX/logs
mkdir -p ${subjdir}.bedpostX/logs/pid_${$}
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
${FSLDIR}/bin/fslslice ${subjdir}/data
${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask
#for parallel processing, the following need to be setup elsewhere
#FSLMACHINELIST="list of machines (can be duplicated for two processors etc.)"
#FSLREMOTECALL="ssh (or rsh or whatever you want to use)"
if [ "x$FSLMACHINELIST" = "x" ] ; then
echo "processing data on local host"
${FSLDIR}/bin/bedpostX_proc $subjdir $nslices -n $nfibres -w $fudge -b $burnin ${subjdir}.bedpostX/logs/pid_${$} &
else
echo "processing data on hosts: $FSLMACHINELIST"
for machine in $FSLMACHINELIST; do
echo "if [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpostX_proc $subjdir $nslices ${subjdir}.bedpostX/logs/pid_${$}; else echo FSLDIR not set in any default location on machine `hostname`;fi"| $FSLREMOTECALL $machine /bin/sh &
done
fi
echo finished
b=0
finished=0;
while [ $finished -eq 0 ];do
b=`expr $b + 1 `
sleep 60;
nfin=`echo ${subjdir}.bedpostX/logs/.*_finished | grep -v ".\*" |wc -w`
if [ $nfin -eq $nslices ];then
finished=1;
fi
if [ $b -eq 10 ]; then
echo "$nfin slices processed"
b=0
fi
done
#postprocessing
#postprocess $subjdir
numfib=`${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples |wc -w`
echo number of fibres $numfib
fib=1;
while [ $fib -le $numfib ];do
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples
${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples
${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpostX/merged_th${fib}samples ${subjdir}.bedpostX/merged_ph${fib}samples ${subjdir}.bedpostX/nodif_brain_mask ${subjdir}.bedpostX/dyads${fib}
fib=`echo "$fib +1"|bc`;
done
echo Removing intermediate files
if [ `imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then
if [ `imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then
if [ `imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then
rm -rf ${subjdir}.bedpostX/diff_slices
rm -f ${subjdir}/data_slice_*
rm -f ${subjdir}/nodif_brain_mask_slice_*
fi
fi
fi
echo Creating identity xfm
xfmdir=${subjdir}.bedpostX/xfms
mkdir -p $xfmdir
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
ExitUnlock
old_bedpost_kill_all deleted 100755 → 0
+ 0
− 14
View file @ 4eb3c4ae
#!/bin/sh
# Copyright (C) 2004 University of Oxford
#
# SHCOPYRIGHT
j=`ps -U $USER |grep -v grep | grep bedpost|grep -v bedpost_kill | awk '{print $1}'`
if [ "x${j}" != "x" ];then
kill -KILL $j
fi
i=`ps -U $USER |grep -v grep | grep diff_pvm| awk '{print $1}'`
if [ "x${i}" != "x" ];then
kill -KILL $i
fi
old_bedpost_kill_pid deleted 100755 → 0
+ 0
− 21
View file @ 4eb3c4ae
#!/bin/sh
# Copyright (C) 2004 University of Oxford
#
# SHCOPYRIGHT
Usage(){
echo "bedpost_kill_pid <pid>"
echo ""
echo "<pid> is the pid of the bedpost_proc"
echo "kills this process + all diff_pvm children"
echo ""
exit
}
[ "$1" = "" ] && Usage
pid=$1
i=`ps -fU $USER |grep -v grep | grep diff_pvm |grep ${pid}| awk '{print $2}'`
kill -KILL $pid $i
old_bedpost_proc deleted 100755 → 0
+ 0
− 39
View file @ 4eb3c4ae
#!/bin/sh
# Copyright (C) 2004 University of Oxford
#
# SHCOPYRIGHT
Usage() {
echo ""
echo "Usage: bedpost_proc <subject_dir> <nslices> [piddir]"
echo ""
exit
}
[ "$2" = "" ] && Usage
[ "$3" = "" ] || touch ${3}/`hostname`_fdt_${$}
subjdir=$1
nslices=$2
slice=0
while [ $slice -lt $nslices ];do
slicezp=`${FSLDIR}/bin/zeropad $slice 4`
if [ ! -f ${subjdir}.bedpost/logs/.$slicezp ] ; then
echo `hostname`_${$} > ${subjdir}.bedpost/logs/.$slicezp
sleep 10
if [ `hostname`_${$} = `cat ${subjdir}.bedpost/logs/.$slicezp | sed -n '1p'` ] ; then
nice ${FSLDIR}/bin/diff_pvm --data=${subjdir}/data_slice_$slicezp --mask=${subjdir}/nodif_brain_mask_slice_$slicezp -b ${subjdir}/bvals -r ${subjdir}/bvecs --logdir=${subjdir}.bedpost/diff_slices/data_slice_$slicezp --nj=1300 --bi=300 --se=20 > ${subjdir}.bedpost/logs/log$slicezp
touch ${subjdir}.bedpost/logs/.${slicezp}_finished
fi
fi
slice=`echo "$slice + 1" | bc`
done
[ "$3" = "" ] || rm ${3}/`hostname`_fdt_${$}
sleep 10
\ No newline at end of file
probtrack.cc deleted 100644 → 0
+ 0
− 77
View file @ 4eb3c4ae
/* Copyright (C) 2004 University of Oxford */
/* CCOPYRIGHT */
#include <iostream>
#include <fstream>
#include "newimage/newimageall.h"
#include "utils/log.h"
#include "meshclass/meshclass.h"
#include "probtrack.h"
using namespace std;
using namespace NEWIMAGE;
using namespace TRACT;
using namespace Utilities;
using namespace PARTICLE;
using namespace TRACTVOLS;
using namespace mesh;
//using namespace NEWMAT;
//////////////////////////
/////////////////////////
int main ( int argc, char **argv ){
probtrackOptions& opts =probtrackOptions::getInstance();
Log& logger = LogSingleton::getInstance();
opts.parse_command_line(argc,argv,logger);
srand(opts.rseed.value());
if(opts.verbose.value()>0){
opts.status();
}
if(opts.mode.value()=="simple")
track();
else if(opts.mode.value()=="seeds_to_targets")
seeds_to_targets();
else if(opts.mode.value()=="seedmask")
alltracts();
else if(opts.mode.value()=="twomasks_symm")
twomasks_symm();
else if(opts.mode.value()=="waypoints")
waypoints();
else if(opts.mode.value()=="matrix1")
matrix1();
else if(opts.mode.value()=="matrix2"){
if(opts.meshfile.value()=="")
matrix2();
else
mesh_matrix2();
}
else if(opts.mode.value()=="maskmatrix")
maskmatrix();
else if(opts.mode.value()=="meshlengths")
mesh_lengths();
else{
cout <<"Invalid setting for option mode -- try setting mode=help"<<endl;
}
return 0;
}
probtrack.h deleted 100644 → 0
+ 0
− 13
View file @ 4eb3c4ae
/* Copyright (C) 2004 University of Oxford */
/* CCOPYRIGHT */
#include "probtrackOptions.h"
#include "particle.h"
#include "tractvols.h"
#include "pt_simple.h"
#include "pt_twomasks.h"
#include "pt_seeds_to_targets.h"
#include "pt_alltracts.h"
#include "pt_matrix.h"
#include "pt_matrix_mesh.h"
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