From 9df2e2dcbf08a9e5e31b7ca08679ff355ffe3211 Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Tue, 13 Oct 2009 11:24:01 +0000
Subject: [PATCH] nonlinear

---
 bedpostx_single_slice.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/bedpostx_single_slice.sh b/bedpostx_single_slice.sh
index cf83870..d844b44 100755
--- a/bedpostx_single_slice.sh
+++ b/bedpostx_single_slice.sh
@@ -6,7 +6,8 @@ fudge=$3
 bi=$4
 njumps=$5
 sampleevery=$6
-slice=$7
+model=$7
+slice=$8
 
 slicezp=`${FSLDIR}/bin/zeropad $slice 4`
 
@@ -15,5 +16,5 @@ ${FSLDIR}/bin/xfibres\
  --mask=$subjdir/nodif_brain_mask_slice_$slicezp\
  -b $subjdir/bvals -r $subjdir/bvecs\
  --forcedir --logdir=$subjdir.bedpostX/diff_slices/data_slice_$slicezp\
- --fudge=$fudge --nj=$njumps --bi=$bi --se=$sampleevery --upe=24 --nfibres=$nfibres > $subjdir.bedpostX/logs/log$slicezp  && echo Done
+ --fudge=$fudge --nj=$njumps --bi=$bi --model=$model --nonlinear --se=$sampleevery --upe=24 --nfibres=$nfibres  > $subjdir.bedpostX/logs/log$slicezp  && echo Done
 
-- 
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