diff --git a/CUDA/bedpostx_multigpu_SGE b/CUDA/bedpostx_multigpu_SGE
deleted file mode 100755
index 90b1244b9f6524ae2f8ef48635fa94b6f12ae70c..0000000000000000000000000000000000000000
--- a/CUDA/bedpostx_multigpu_SGE
+++ /dev/null
@@ -1,315 +0,0 @@
-#!/bin/bash
-
-# Copyright (C) 2004 University of Oxford
-#
-# SHCOPYRIGHT
-
-
-if [ -z $PE_NAME ] ; then
- echo "Please set PE_NAME environment variable with your Parallel Environment List name used in SGE for GPUs slots"
- exit 1
-fi
-
-if [ -z $QUEUE_GPU ] ; then
- echo "Please set QUEUE_GPU environment variable with a Queue Instance name used in SGE for process slices in GPUs"
- exit 1
-fi
-
-if [ -z $QUEUE_GENERAL ] ; then
- echo "Please set QUEUE_GENERAL environment variable with a Queue Instance name used in SGE for process the post processing stage in CPU"
- exit 1
-fi
-
-beforet=`date +%s`
-if [ "x$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 "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 ""
- 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
-}
-
-
-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 $subjdir
-
-# this is the name of cuda queue
-queue=${QUEUE_GPU}
-#this is the name of general queue
-queue2=${QUEUE_GENERAL}
-
-#parse option arguments
-nfibres=2
-fudge=1
-burnin=1000
-njumps=1250
-sampleevery=25
-model=1
-gflag=0
-f0=0
-rician=0
-
-shift
-while [ ! -z "$1" ]
-do
- case "$1" in
- -n) nfibres=$2;shift;;
- --nf=?) nfibres=`echo $1 | sed s/"--nf="//g`;;
- --model=?) model=`echo $1 | sed s/"--model="//g`;;
- -w) fudge=$2;shift;;
- -b) burnin=$2;shift;;
- -j) njumps=$2;shift;;
- -s) sampleevery=$2;shift;;
- --f0) f0=1 others="$others $1";;
- --rician) rician=1 others="$others $1";;
- -model) model=$2;shift;;
- -g) gflag=1;;
- *) others="$others $1";;
- esac
- shift
-done
-
-opts="--nf=$nfibres --fudge=$fudge --bi=$burnin --nj=$njumps --se=$sampleevery --model=$model"
-defopts="--cnonlinear"
-opts="$opts $defopts $others"
-
-#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 [ ${gflag} -eq 1 ]; then
- if [ `${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
-
-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
-
-if [ ${gflag} -eq 1 ]; then
- echo "bedpostx_multigpu_SGE "${subjdir} $opts "-g" >> ${subjdir}.bedpostX/commands.txt
-else
- echo "bedpostx_multigpu_SGE "${subjdir} $opts >> ${subjdir}.bedpostX/commands.txt
-fi
-
-
-echo "..............Compiling CUDA-gpu code .................."
-
-export LD_LIBRARY_PATH=${CUDA}/lib64:${subjdir}.bedpostX:${CUDA}/lib:$LD_LIBRARY_PATH
-export DYLD_LIBRARY_PATH=${CUDA}/lib64:${subjdir}.bedpostX:${CUDA}/lib:$LD_LIBRARY_PATH
-export PATH=${FSLDIR}/bin:$PATH
-
-volumes=`${FSLDIR}/bin/fslval ${subjdir}/data dim4`
-echo "DIRECTIONS NUMBER: $volumes"
-
-filename="${subjdir}.bedpostX/options.h"
-
-if [ $volumes -le 64 ]; then
- threadsBlock=$volumes
-else
- threadsBlock=64
-fi
-
-params=$((2+3*$nfibres))
-
-if [ $f0 -eq 1 ]; then
- params=$(($params+1))
-fi
-
-if [ $model -eq 2 ]; then
- params=$(($params+1))
-fi
-
-if [ $rician -eq 1 ]; then
- params=$(($params+1))
-fi
-
-rem=$(($volumes%$threadsBlock))
-maxndirs=$(($volumes/$threadsBlock))
-
-if [ $rem -ne 0 ]; then
- maxndirs=$(($maxndirs+1))
-fi
-
-dstd=$(($model-1));
-
-params_rep=$(($params-1))
-params_step0_m2_rep=$(($params_step0_m2-1))
-
-echo "#define NDIRECTIONS $volumes
-#define NFIBRES $nfibres
-#define NPARAMS $params
-#define MAXNDIRS_PER_THREAD $maxndirs
-#define THREADS_BLOCK $threadsBlock">$filename
-
-before=`date +%s`
-
-${CUDA}/bin/nvcc --shared --compiler-options '-fPIC' -o ${subjdir}.bedpostX/libbedpostx_cuda.so ${FSLDIR}/src/fdt/CUDA/init_gpu.cu ${FSLDIR}/src/fdt/CUDA/samples.cu ${FSLDIR}/src/fdt/CUDA/diffmodels.cu ${FSLDIR}/src/fdt/CUDA/runmcmc.cu ${FSLDIR}/src/fdt/CUDA/xfibres_gpu.cu -O3 -arch sm_20 -lcudart -lcuda -lcurand -L${CUDA}/lib64 -L${CUDA}/lib -I${subjdir}.bedpostX -I${FSLDIR}/extras/include/newmat -I${FSLDIR}/extras/include/boost -I${FSLDIR}/include -I${CUDA}/include/thrust -I${FSLDIR}/src/fdt
-
-file=${subjdir}.bedpostX/libbedpostx_cuda.so
-
-if [ -f $file ];
-then
-after=`date +%s`
-diff=$(($after-$before))
-echo "Compilation Time: $diff seconds" >> ${subjdir}.bedpostX/times
-
-echo "CUDA CODE compiled successfully"
-
-mailto=`whoami`@fmrib.ox.ac.uk
-before=`date +%s`
-echo Preprocessing stages
-${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}
-
-after=`date +%s`
-diff=$(($after-$before))
-echo "Preprocessing Time: $diff seconds" >> ${subjdir}.bedpostX/times
-
-before=`date +%s`
-nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
-
-slice=0
-
-post_string="qsub -q $queue2 -N postproc -V -b y"
-
-
-echo Submitting slices to GPUs
-while [ $slice -lt $nslices ];do
-
- job=`qsub -q $queue -pe $PE_NAME 1 -N "Bedpostx" -V -b y -o ${subjdir}.bedpostX/logs/output -e ${subjdir}.bedpostX/logs/error ${FSLDIR}/bin/splitter_multigpu $subjdir $gflag $nfibres $slice $opts`
-
- IFS=" "
- array=( $job )
- job_id=${array[2]}
-
- #echo "JOB: "$job_id
-
- post_string="$post_string -hold_jid $job_id"
-
- slice=$(($slice + 1))
-done
-
-post_string="$post_string -o ${subjdir}.bedpostX/logs/output -e ${subjdir}.bedpostX/logs/error ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir"
-#echo $post_string
-$post_string
-
-
-echo "All jobs submitted"
-
-finished=0
-logdir=${subjdir}.bedpostX/logs
-tim=0
-
-while [ $finished -eq 0 ] ; do
- nfin=0
- pslice=0
- while [ $pslice -lt $nslices ];do
- slicezp=`${FSLDIR}/bin/zeropad $pslice 4`
- isimg=`${FSLDIR}/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_$slicezp/dyads1`
- if [ $isimg -eq 1 ];then
- nfin=$(($nfin + 1))
- fi
- pslice=$(($pslice + 1))
- done
- echo $nfin "slices processed"
-
- if [ $tim -eq 0 ] ; then
- if [ $nfin -eq $nslices ] ; then
- after=`date +%s`
- diff=$(($after-$before))
- echo "Execution Time: $diff seconds" >> ${subjdir}.bedpostX/times
- tim=1
- fi
- fi
-
- if [ -f ${subjdir}.bedpostX/xfms/eye.mat ] ; then
- finished=1
- echo "All slices processed"
- fi
- sleep 15;
-done
-
-
-
-aftert=`date +%s`
-diff=$(($aftert-$beforet))
-echo "TOTAL Time: $diff seconds" >> ${subjdir}.bedpostX/times
-
-else
- echo
- echo
- echo "CUDA COMPILER ERROR. Please be sure that you have set correctly CUDA environment variable with your CUDA path"
- echo
-fi