Postprocessing of the parts created by the BedpostX GPU version

CUDA/bedpostx_postproc_gpu.sh

+#!/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