From d455fb629df0c4dfd3637d449efe461ece89d29e Mon Sep 17 00:00:00 2001
From: Moises Fernandez <moisesf@fmrib.ox.ac.uk>
Date: Mon, 24 Jun 2013 11:04:28 +0000
Subject: [PATCH] Fix name of some variables
---
rubix_parallel.sh | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/rubix_parallel.sh b/rubix_parallel.sh
index f702494..d83e369 100644
--- a/rubix_parallel.sh
+++ b/rubix_parallel.sh
@@ -179,7 +179,7 @@ else
fi
fi
fi
-exit 1
+
echo Making rubix directory structure
mkdir -p ${subjdir}.rubiX
@@ -200,11 +200,11 @@ echo Queuing parallel processing stage
if [ ${gflag} -eq 1 ]; then
opts="$opts --gLR=${subjdir}.rubiX/grad_devLR_slice_${slicezp} --gHR=${subjdir}.rubiX/grad_devHR_newslice_${slicezp}"
fi
- echo "$devel_dir/rubix --dLR=${subjdir}.rubiX/dataLR_slice_${slicezp} --mLR=${subjdir}.rubiX/nodif_brain_maskLR_slice_${slicezp} --rLR=${subjdir}.rubiX/bvecsLR --bLR=${subjdir}.rubiX/bvalsLR --dHR=${subjdir}.rubiX/dataHR_newslice_${slicezp} --rHR=${subjdir}.rubiX/bvecsHR --bHR=${subjdir}.rubiX/bvalsHR --forcedir --nf=$nfibres --nM=$nModes --bi=$burnin --model=$modelnum --logdir=${subjdir}.rubiX/diff_slices/data_slice_$slicezp ${opts}" >> ${subjdir}.rubiX/commands.txt
+ echo "$devel_dir/rubix --dLR=${subjdir}.rubiX/dataLR_slice_${slicezp} --mLR=${subjdir}.rubiX/nodif_brain_maskLR_slice_${slicezp} --rLR=${subjdir}.rubiX/bvecsLR --bLR=${subjdir}.rubiX/bvalsLR --dHR=${subjdir}.rubiX/dataHR_newslice_${slicezp} --rHR=${subjdir}.rubiX/bvecsHR --bHR=${subjdir}.rubiX/bvalsHR --forcedir --nf=$nfibres --nM=$nmodes --bi=$burnin --model=$model --logdir=${subjdir}.rubiX/diff_slices/data_slice_$slicezp ${opts}" >> ${subjdir}.rubiX/commands.txt
slice=$(($slice + 1))
done
RubiXid=`${FSLDIR}/bin/fsl_sub -T 1400 -j $preprocid -l ${subjdir}.rubiX/logs -N rubix -t ${subjdir}.rubiX/commands.txt`
echo Queuing post processing stage
- mergeid=`${FSLDIR}/bin/fsl_sub -T 60 -R 8000 -j $RubiXid -N rubix_post -l ${subjdir}.rubiX/logs $script_dir/rubix_postproc.sh ${subjdir} ${filterflag}`
\ No newline at end of file
+ mergeid=`${FSLDIR}/bin/fsl_sub -T 60 -R 8000 -j $RubiXid -N rubix_post -l ${subjdir}.rubiX/logs $script_dir/rubix_postproc.sh ${subjdir} ${filterflag}`
--
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