/
bedpostx_postproc_gpu.sh
executable file
·73 lines (58 loc) · 2.41 KB
/
bedpostx_postproc_gpu.sh
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#!/bin/bash
# Copyright (C) 2012 University of Oxford
#
# SHCOPYRIGHT
# last 2 parameters are subjdir and bindir
parameters=""
while [ ! -z "${2+x}" ]
do
case $1 in
"--nf="*) numfib=`echo $1 | cut -d '=' -f2` ;;
esac
all=$all" "$1
subjdir=$1
shift
done
bindir=$1
$bindir/bin/merge_parts_gpu $all
fib=1
while [ $fib -le $numfib ]
do
${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}/nodif_brain_mask ${subjdir}.bedpostX/dyads${fib}
if [ $fib -ge 2 ];then
${FSLDIR}/bin/maskdyads ${subjdir}.bedpostX/dyads${fib} ${subjdir}.bedpostX/mean_f${fib}samples
${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f${fib}samples -div ${subjdir}.bedpostX/mean_f1samples ${subjdir}.bedpostX/mean_f${fib}_f1samples
${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/dyads${fib}_thr0.05 -mul ${subjdir}.bedpostX/mean_f${fib}_f1samples ${subjdir}.bedpostX/dyads${fib}_thr0.05_modf${fib}
${FSLDIR}/bin/imrm ${subjdir}.bedpostX/mean_f${fib}_f1samples
fi
fib=$(($fib + 1))
done
if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/mean_f1samples` -eq 1 ];then
${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_f1samples -mul 0 ${subjdir}.bedpostX/mean_fsumsamples
fib=1
while [ $fib -le $numfib ]
do
${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/mean_fsumsamples -add ${subjdir}.bedpostX/mean_f${fib}samples ${subjdir}.bedpostX/mean_fsumsamples
fib=$(($fib + 1))
done
fi
echo Removing intermediate files
if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then
if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then
if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then
rm -rf "${subjdir}.bedpostX/diff_parts"
rm -rf "${subjdir}.bedpostX/data"*
rm -rf "${subjdir}.bedpostX/grad_dev"*
fi
fi
fi
echo Creating identity xfm
xfmdir=${subjdir}.bedpostX/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