From c1a12e7a1098cb30470ef6ff8ebab3e366650fdd Mon Sep 17 00:00:00 2001
From: Tim Behrens <behrens@fmrib.ox.ac.uk>
Date: Thu, 26 Aug 2004 12:15:47 +0000
Subject: [PATCH] *** empty log message ***
---
old_bedpost | 11 +++++++++++
old_bedpost_proc | 12 +++++++-----
2 files changed, 18 insertions(+), 5 deletions(-)
diff --git a/old_bedpost b/old_bedpost
index d6abde3..3f98c64 100755
--- a/old_bedpost
+++ b/old_bedpost
@@ -182,6 +182,17 @@ done
#postprocessing
#postprocess $subjdir
+##this will have to change..
+echo "Merging outputs into 4D files"
+
+${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples.hdr.gz`
+${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples.hdr.gz`
+${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_fsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/f_samples.hdr.gz`
+${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_thsamples -Tmean ${subjdir}.bedpost/mean_thsamples
+${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_phsamples -Tmean ${subjdir}.bedpost/mean_phsamples
+${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_fsamples -Tmean ${subjdir}.bedpost/mean_fsamples
+
+
mkdir -p ${subjdir}.bedpost/xfms
xfmdir=${subjdir}.bedpost/xfms
echo 1 0 0 0 > ${xfmdir}/eye.mat
diff --git a/old_bedpost_proc b/old_bedpost_proc
index de71c53..2a7c806 100755
--- a/old_bedpost_proc
+++ b/old_bedpost_proc
@@ -15,15 +15,17 @@ Usage() {
subjdir=$1
nslices=$2
+## Do the zeropadding tim
slice=0
while [ $slice -lt $nslices ];do
- if [ ! -e ${subjdir}.bedpost/logs/.$slice ] ; then
- echo `hostname`_${$} > ${subjdir}.bedpost/logs/.$slice
+ slicezp=`zeropad $slice 4`
+ if [ ! -e ${subjdir}.bedpost/logs/.$slicezp ] ; then
+ echo `hostname`_${$} > ${subjdir}.bedpost/logs/.$slicezp
sleep 10
- if [ `hostname`_${$} = `cat ${subjdir}.bedpost/logs/.$slice | sed -n '1p'` ] ; then
- nice ${FSLDIR}/bin/diff_pvm --data=${subjdir}/data_slice_$slice --mask=${subjdir}/nodif_brain_mask_slice_$slice -b ${subjdir}/bvals -r ${subjdir}/bvecs --logdir=${subjdir}.bedpost/diff_slices/data_slice_$slice --nj=1300 --bi=300 --se=20 > ${subjdir}.bedpost/logs/log$slice
- touch ${subjdir}.bedpost/logs/.${slice}_finished
+ if [ `hostname`_${$} = `cat ${subjdir}.bedpost/logs/.$slicezp | sed -n '1p'` ] ; then
+ nice ${FSLDIR}/bin/diff_pvm --data=${subjdir}/data_slice_$slicezp --mask=${subjdir}/nodif_brain_mask_slice_$slicezp -b ${subjdir}/bvals -r ${subjdir}/bvecs --logdir=${subjdir}.bedpost/diff_slices/data_slice_$slicezp --nj=1300 --bi=300 --se=20 > ${subjdir}.bedpost/logs/log$slicezp
+ touch ${subjdir}.bedpost/logs/.${slicezp}_finished
fi
fi
slice=`echo "$slice + 1" | bc`
--
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