From 553cc3476cc655990a5c289830f6bdeafb1822b9 Mon Sep 17 00:00:00 2001
From: Moises Fernandez <moisesf@fmrib.ox.ac.uk>
Date: Mon, 24 Jun 2013 13:08:22 +0000
Subject: [PATCH] Add FSL path to some commands
---
rubix_preproc.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/rubix_preproc.sh b/rubix_preproc.sh
index f797f7a..222983c 100644
--- a/rubix_preproc.sh
+++ b/rubix_preproc.sh
@@ -13,7 +13,7 @@ if [ ${filterflag} -eq 1 ]; then
cp ${subjdir}/bvecs $out_dir/bvecsHR
cp ${subjdir}/bvals $out_dir/bvalsHR
${FSLDIR}/bin/fslslice $subjdir/data $out_dir/dataHR
- HighRes=`fslval ${subjdir}/data pixdim1`
+ HighRes=`${FSLDIR}/bin/fslval ${subjdir}/data pixdim1`
LowRes=`echo "${HighRes} * 2" | bc -l`
echo "Create Downsampled version of data at ${LowRes} mm isotropic"
${FSLDIR}/bin/flirt -in ${subjdir}/nodif_brain_mask -ref ${subjdir}/nodif_brain_mask -applyisoxfm ${LowRes} -interp nearestneighbour -out ${out_dir}/nodif_brain_maskLR
--
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