[Neurodebian-users] FSL randomise_parallel has a bashism that causes the defragmentation step to fail under dash

[Chase,Philip B]

I submitted a bug report to bugs.debian.org

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=693373

Philip

Philip B. Chase
Assistant Director
Clinical and Translational Science IT
University of Florida
pbc at ufl.edu
352-294-5164

From: <Chase>, Philip Chase <pbc at ufl.edu<mailto:pbc at ufl.edu>>
Date: Tuesday, November 6, 2012 3:03 PM
To: "neurodebian-users at lists.alioth.debian.org<mailto:neurodebian-users at lists.alioth.debian.org>" <neurodebian-users at lists.alioth.debian.org<mailto:neurodebian-users at lists.alioth.debian.org>>
Subject: [Neurodebian-users] FSL randomise_parallel has a bashism that causes the defragmentation step to fail under dash

Where should I report a bug in FSL—neurodebian packaged fsl-5.0, 5.0.0-1~nd60+1 ?

I found a bug in randomise_parallel that causes the defragmentation step to fail at the end of the randomise run.  The error  log of the defragment job shows

./GM_mod_merg_s3.defragment: 15: Bad substitution
./GM_mod_merg_s3.defragment: 15: Bad substitution
...
./GM_mod_merg_s3.defragment: 15: Bad substitution

If the shell is changed from dash to bash the defragment jobs works fine.  This patch does the trick:

diff --git a/randomise_parallel b/randomise_parallel
index dc112c9..589033c 100755
--- a/randomise_parallel
+++ b/randomise_parallel
@@ -128,7 +128,7 @@ GENERATE_ID=`$FSLDIR/bin/fsl_sub -T ${REQUESTED_TIME} -N ${BASENAME}.generate -l

 #stage2:
 cat <<combineScript > ${DIRNAME}/${BASENAME}.defragment
-#!/bin/sh
+#!/bin/bash
 echo "Merging stat images"
 for FIRSTSEED in ${ROOTNAME}_SEED1_*_p_*.nii.gz ${ROOTNAME}_SEED1_*_corrp_*.nii.gz ; do
   ADDCOMMAND=""

Where do I report this?  FSL seems to have no bug reporting mechanism, while http://neuro.debian.net/pkgs/fsl.html directs me to this list and not a bug reporting site.

Thanks,
Philip

Philip B. Chase
Assistant Director
Clinical and Translational Science IT
University of Florida
pbc at ufl.edu<mailto:pbc at ufl.edu>
352-294-5164
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