Package: fsl-5.0
Version: 5.0.0-1~nd60+1
Severity: normal
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=""
-- System Information:
Debian Release: 6.0.5
APT prefers stable
APT policy: (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.32-5-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_US, LC_CTYPE=en_US (charmap=ISO-8859-1)
Shell: /bin/sh linked to /bin/dash
Versions of packages fsl-5.0 depends on:
ii bc 1.06.95-2 The GNU bc arbitrary precision cal
ii chromium-br 6.0.472.63~r59945-5+squeeze6 Chromium browser
ii dc 1.06.95-2 The GNU dc arbitrary precision rev
ii epiphany-br 2.30.6-1 Intuitive GNOME web browser
ii google-chro 23.0.1271.64-r165188 The web browser from Google
ii iceweasel [ 3.5.16-17 Web browser based on Firefox
ii libc6 2.11.3-3 Embedded GNU C Library: Shared lib
ii libexpat1 2.0.1-7+squeeze1 XML parsing C library - runtime li
ii libgcc1 1:4.4.5-8 GCC support library
ii libgd2-noxp 2.0.36~rc1~dfsg-5 GD Graphics Library version 2 (wit
ii libgdchart- 0.11.5-7 Generate graphs using the GD libra
ii libgiftiio0 1.0.9-1 IO library for the GIFTI cortical
ii libgl1-mesa 7.7.1-5 A free implementation of the OpenG
ii libglu1-mes 7.7.1-5 The OpenGL utility library (GLU)
ii libnewmat10 1.10.4-5 matrix manipulations library (C++)
ii libnifti2 2.0.0-1 IO libraries for the NIfTI-1 data
ii libpng12-0 1.2.44-1+squeeze4 PNG library - runtime
ii libstdc++6 4.4.5-8 The GNU Standard C++ Library v3
ii python 2.6.6-3+squeeze7 interactive high-level object-orie
ii tcl8.4 8.4.19-4 Tcl (the Tool Command Language) v8
ii tcsh [c-she 6.17.02-4 TENEX C Shell, an enhanced version
ii tk8.4 8.4.19-4 Tk toolkit for Tcl and X11, v8.4 -
ii w3m [www-br 0.5.2-9 WWW browsable pager with excellent
ii zlib1g 1:1.2.3.4.dfsg-3 compression library - runtime
Versions of packages fsl-5.0 recommends:
ii fsl-atlases 5.0.0-2 FSL's MNI152 standard space stereo
ii fsl-doc-5.0 5.0.0-1~nd60+1 documentation for FSL
ii fslview 3.1.8+4.1.9-1~nd60+1 viewer for (f)MRI and DTI data
Versions of packages fsl-5.0 suggests:
ii dicomnifti 2.30.0-1~nd60+1 converts DICOM files into the NIfT
ii fsl-feeds 5.0.0-1 FSL Evaluation and Example Data Su
ii fsl-first-data 5.0.0-2 model data for FIRST subcortical b
ii fsl-possum-data 5.0.0-2 sequence templates for the POSSUM
pn gridengine-client <none> (no description available)
pn octave | octave3.2 <none> (no description available)
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