From fe882b3e00cd8623833e2b5b41c950b990ef1a64 Mon Sep 17 00:00:00 2001
From: David Flitney <dave.flitney@ndcn.ox.ac.uk>
Date: Fri, 30 Nov 2007 13:58:34 +0000
Subject: [PATCH] mods to remove shell comment directives from bedpost
---
bedpostx | 4 ++--
bedpostx_postproc.sh | 7 -------
bedpostx_preproc.sh | 7 -------
bedpostx_single_slice.sh | 9 ---------
4 files changed, 2 insertions(+), 25 deletions(-)
diff --git a/bedpostx b/bedpostx
index bd060f6..bd9fa42 100755
--- a/bedpostx
+++ b/bedpostx
@@ -104,7 +104,7 @@ mkdir -p ${subjdir}.bedpostX/xfms
mailto=`whoami`@fmrib.ox.ac.uk
echo Queuing preprocessing stages
-preprocid=`${FSLDIR}/bin/fsl_sub -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}`
+preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}`
echo Queuing parallel processing stage
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
@@ -146,7 +146,7 @@ bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $m
[ "x$SGE_ROOT" = "x" ] && kill $monitorpid
echo Queuing post processing stage
-mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
+mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
if [ "x$SGE_ROOT" != "x" ]; then
echo
diff --git a/bedpostx_postproc.sh b/bedpostx_postproc.sh
index 302b7d1..180cee9 100755
--- a/bedpostx_postproc.sh
+++ b/bedpostx_postproc.sh
@@ -1,12 +1,5 @@
#!/bin/sh
-#$ -cwd
-#$ -q short.q
-#$ -S /bin/sh
-#$ -V
-#$ -N bpx_postproc
-#$ -m ae
-
subjdir=$1
numfib=`${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples | wc -w | awk '{print $1}'`
diff --git a/bedpostx_preproc.sh b/bedpostx_preproc.sh
index 90123ca..0fab6d4 100755
--- a/bedpostx_preproc.sh
+++ b/bedpostx_preproc.sh
@@ -1,12 +1,5 @@
#!/bin/sh
-#$ -cwd
-#$ -q short.q
-#$ -S /bin/sh
-#$ -V
-#$ -N bpx_preproc
-#$ -m as
-
subjdir=$1
echo Copying files to bedpost directory
diff --git a/bedpostx_single_slice.sh b/bedpostx_single_slice.sh
index 8934d1a..cf83870 100755
--- a/bedpostx_single_slice.sh
+++ b/bedpostx_single_slice.sh
@@ -1,13 +1,5 @@
#!/bin/sh
-#$ -cwd
-#$ -q long.q
-#$ -S /bin/sh
-#$ -V
-#$ -N bedpostx
-#$ -m n
-#$ -o $1.bedpostX/logs -e $1.bedpostX/logs
-
subjdir=$1
nfibres=$2
fudge=$3
@@ -16,7 +8,6 @@ njumps=$5
sampleevery=$6
slice=$7
-
slicezp=`${FSLDIR}/bin/zeropad $slice 4`
${FSLDIR}/bin/xfibres\
--
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