From 2c33ff6d667a27e650276b50a675ec4588cff9bf Mon Sep 17 00:00:00 2001
From: Moises Fernandez <moisesf@fmrib.ox.ac.uk>
Date: Mon, 24 Jun 2013 10:25:05 +0000
Subject: [PATCH] Add FSL path to some commands
---
rubix_preproc.sh | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/rubix_preproc.sh b/rubix_preproc.sh
index 85c55b6..6a5cfd1 100644
--- a/rubix_preproc.sh
+++ b/rubix_preproc.sh
@@ -16,11 +16,11 @@ if [ ${filterflag} -eq 1 ]; then
HighRes=`fslval ${subjdir}/data pixdim1`
LowRes=`echo "${HighRes} * 2" | bc -l`
echo "Create Downsampled version of data at ${LowRes} mm isotropic"
- flirt -in ${subjdir}/nodif_brain_mask -ref ${subjdir}/nodif_brain_mask -applyisoxfm ${LowRes} -interp nearestneighbour -out ${out_dir}/nodif_brain_maskLR
- flirt -in ${subjdir}/data -ref ${subjdir}/data -applyisoxfm ${LowRes} -interp sinc -out ${out_dir}/dataLR
+ ${FSLDIR}/bin/flirt -in ${subjdir}/nodif_brain_mask -ref ${subjdir}/nodif_brain_mask -applyisoxfm ${LowRes} -interp nearestneighbour -out ${out_dir}/nodif_brain_maskLR
+ ${FSLDIR}/bin/flirt -in ${subjdir}/data -ref ${subjdir}/data -applyisoxfm ${LowRes} -interp sinc -out ${out_dir}/dataLR
if [ ${gflag} -eq 1 ]; then
echo "Create Downsampled version of grad_dev at ${LowRes} mm isotropic"
- flirt -in ${subjdir}/grad_dev -ref ${subjdir}/grad_dev -applyisoxfm ${LowRes} -interp nearestneighbour -out ${out_dir}/grad_devLR
+ ${FSLDIR}/bin/flirt -in ${subjdir}/grad_dev -ref ${subjdir}/grad_dev -applyisoxfm ${LowRes} -interp nearestneighbour -out ${out_dir}/grad_devLR
${FSLDIR}/bin/fslslice $subjdir/grad_dev $out_dir/grad_devHR
${FSLDIR}/bin/fslslice ${out_dir}/grad_devLR $out_dir/grad_devLR
fi
@@ -63,9 +63,9 @@ do
count=$(($count - 1))
arr_cnt=$(($arr_cnt + 1))
done
- fslmerge -z ${out_dir}/dataHR_newslice_${slicezp} `echo ${filenames[*]}`
+ ${FSLDIR}/bin/fslmerge -z ${out_dir}/dataHR_newslice_${slicezp} `echo ${filenames[*]}`
if [ ${gflag} -eq 1 ]; then
- fslmerge -z ${out_dir}/grad_devHR_newslice_${slicezp} `echo ${gfilenames[*]}`
+ ${FSLDIR}/bin/fslmerge -z ${out_dir}/grad_devHR_newslice_${slicezp} `echo ${gfilenames[*]}`
fi
slice=$(($slice + 1))
done
--
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