From 03b7cb37402c64247def9160b4a31bacd53a1852 Mon Sep 17 00:00:00 2001
From: Rita Nunes <rita@fmrib.ox.ac.uk>
Date: Wed, 6 Oct 2004 13:34:54 +0000
Subject: [PATCH] changed the script to be compatible with any image format
---
remove_vols | 38 +++++++++++++++-----------------------
1 file changed, 15 insertions(+), 23 deletions(-)
diff --git a/remove_vols b/remove_vols
index 79ad1ff..933e398 100755
--- a/remove_vols
+++ b/remove_vols
@@ -21,7 +21,7 @@ input_file=$1
output_file=$2
current_dir=`pwd`
-if [ ! -e $input_file.hdr ]; then
+if [ ! `imtest $input_file` ]; then
echo Cant find $input_file
exit
fi
@@ -36,7 +36,7 @@ if [ ! -e bvecs ]; then
exit
fi
-avwsplit $input_file.hdr
+avwsplit $input_file
vol=0
num_vols=`expr $# - 2`
@@ -51,39 +51,31 @@ while [ $vol -lt $num_vols ]; do
v=$3
shift
- if [ -e vol000${v}.hdr ]; then
- rm vol000${v}.hdr -f
- rm vol000${v}.img -f
+ if [ `imtest vol000${v}` ]; then
+ imrm vol000${v}
fi
- if [ -e vol00${v}.hdr ]; then
- rm vol00${v}.hdr -f
- rm vol00${v}.img -f
+ if [ `imtest vol00${v}` ]; then
+ imrm vol00${v}
fi
echo $v > tmp1
cat dodgy_vols tmp1 > tmp2
cat tmp2 > dodgy_vols
+ rm tmp* -f
vol=`expr $vol + 1`
done
-echo "addpath('/usr/people/dtiuser/etc/FMRIB_bvals_bvecs/')">tmp3
-echo "remove_vols('$current_dir')">tmp4
-cat tmp3 tmp4 >tmp.m
-cat tmp.m | matlab
-rm tmp* -f
+echo Removing dodgy volumes from bvals and bvecs
+matlab -nodisplay -nojvm -nosplash 1> matlab.out1 2>&1 <<EOF
+ addpath('/usr/people/dtiuser/etc/FMRIB_bvals_bvecs/');
+ remove_vols('$current_dir');
+ exit
+EOF
+rm matlab.out1 -f
echo "Merging Volumes"
-avwmerge -t $output_file vol*.hdr
+avwmerge -t $output_file `$FSLDIR/bin/imglob -oneperimage vol*`
rm vol* -f
rm dodgy_vols -f
-
-
-
-
-
-
-
-
-
--
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