From 4a399c9a792b091d5d60805807ff6ac3330e89cf Mon Sep 17 00:00:00 2001
From: Moises Fernandez <moisesf@fmrib.ox.ac.uk>
Date: Thu, 11 Apr 2013 16:37:42 +0000
Subject: [PATCH] Postprocessing of the parts created by the BedpostX GPU
version
---
CUDA/bedpostx_postproc_gpu.sh | 67 +++++++++++++++++++++++++++++++++++
1 file changed, 67 insertions(+)
create mode 100644 CUDA/bedpostx_postproc_gpu.sh
diff --git a/CUDA/bedpostx_postproc_gpu.sh b/CUDA/bedpostx_postproc_gpu.sh
new file mode 100644
index 0000000..608a55a
--- /dev/null
+++ b/CUDA/bedpostx_postproc_gpu.sh
@@ -0,0 +1,67 @@
+#!/bin/sh
+
+# Copyright (C) 2012 University of Oxford
+#
+# SHCOPYRIGHT
+
+subjdir=${@:${#@}}
+
+for arg in $@;
+do
+ if [[ $arg =~ "--nf=" ]]; then
+ numfib=`echo $arg | cut -d '=' -f2`
+ fi
+done
+
+${FSLDIR}/bin/merge_parts_gpu $@
+
+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
+ 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_fsamples
+ fib=1
+ while [ $fib -le $numfib ]
+ do
+ fslmaths ${subjdir}.bedpostX/mean_fsamples -add ${subjdir}.bedpostX/mean_f${fib}samples ${subjdir}.bedpostX/mean_fsamples
+ fib=$(($fib + 1))
+ done
+fi
+
+
+
+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_parts
+ if [ `imtest ${subjdir}.bedpostX/grad_dev_slice_0000` -eq 1 ];then
+ rm -f ${subjdir}.bedpostX/grad_dev_slice_*
+ fi
+ fi
+ fi
+fi
+
+echo Creating identity xfm
+
+xfmdir=${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
--
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