removed

my_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 -le $nslices ]
-do
-    echo "${FSLDIR}/bin/my_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

my_bedpostx_single_slice.sh

-#!/bin/sh
-
-subjdir=$1
-nfibres=$2
-fudge=$3
-bi=$4
-njumps=$5
-sampleevery=$6
-slice=$7
-
-slicezp=`${FSLDIR}/bin/zeropad $slice 4`
-
-${FSLDIR}/bin/xfibres\
- --data=$subjdir/data_slice_$slicezp\
- --mask=$subjdir/nodif_brain_mask_slice_$slicezp\
- -b $subjdir/bvals -r $subjdir/bvecs\
- --forcedir --logdir=$subjdir.bedpostX/diff_slices/data_slice_$slicezp\
- --fudge=$fudge --nj=$njumps --bi=$bi --se=$sampleevery --upe=24 --nfibres=$nfibres --allard > $subjdir.bedpostX/logs/log$slicezp  && echo Done
-