From 0def35fd79b584f58449590e018947665b658dc9 Mon Sep 17 00:00:00 2001
From: Moises Fernandez <moisesf@fmrib.ox.ac.uk>
Date: Mon, 29 Apr 2013 11:17:10 +0000
Subject: [PATCH] Delete some SGE not util checks and reorder options prints
---
CUDA/bedpostx_multigpu_LSF | 15 +++------------
1 file changed, 3 insertions(+), 12 deletions(-)
diff --git a/CUDA/bedpostx_multigpu_LSF b/CUDA/bedpostx_multigpu_LSF
index 4555295..3b6cf60 100755
--- a/CUDA/bedpostx_multigpu_LSF
+++ b/CUDA/bedpostx_multigpu_LSF
@@ -6,14 +6,6 @@
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${FSLDIR}/lib
-if [ "x$SGE_ROOT" = "x" ] ; then
- if [ -f /usr/local/share/sge/default/common/settings.sh ] ; then
- . /usr/local/share/sge/default/common/settings.sh
- elif [ -f /usr/local/sge/default/common/settings.sh ] ; then
- . /usr/local/sge/default/common/settings.sh
- fi
-fi
-
Usage() {
echo ""
echo "Usage: bedpostx <subject directory> [options]"
@@ -21,7 +13,9 @@ Usage() {
echo "expects to find bvals and bvecs in subject directory"
echo "expects to find data and nodif_brain_mask in subject directory"
echo "expects to find grad_dev in subject directory, if -g is set"
- echo "options (old syntax)"
+ echo ""
+ echo "<options>:"
+ echo "-NJOBS (number of jobs to queue, the data is divided in NJOBS parts, usefull for a GPU cluster, default 1)"
echo "-n (number of fibres per voxel, default 2)"
echo "-w (ARD weight, more weight means less secondary fibres per voxel, default 1)"
echo "-b (burnin period, default 1000)"
@@ -29,7 +23,6 @@ Usage() {
echo "-s (sample every, default 25)"
echo "-model (1 for monoexponential, 2 for multiexponential, default 1)"
echo "-g (consider gradient nonlinearities, default off)"
- echo "-NJOBS (number of jobs to queue, the data is divided in NJOBS parts, usefull for a GPU cluster, default 1)"
echo ""
echo ""
echo "ALTERNATIVELY: you can pass on xfibres options onto directly bedpostx"
@@ -140,8 +133,6 @@ else
echo "bedpostx_multigpu_LSF "${subjdir} $opts >> ${subjdir}.bedpostX/commands.txt
fi
-mailto=`whoami`@fmrib.ox.ac.uk
-
echo Copying files to bedpost directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
${FSLDIR}/bin/imcp ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
--
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