Your message dated Thu, 03 Feb 2011 14:32:42 +0000
with message-id <[email protected]>
and subject line Bug#611374: fixed in mricron 0.20101102.1~dfsg.1-2
has caused the Debian Bug report #611374,
regarding mricron doesn't find FSL's bet executable
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
611374: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=611374
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: mricron
Version: 0.20101102.1~dfsg.1-1
Severity: normal
Relaying a user bug report that came via email (not mentioning the origin
yet as I'm waiting for approval):
> To reproduce:
> 1. go to About-Preferences and enable the drawing menus
> 2. Draw - Advanced - Brain extraction ; click 'go'
>
> It seems the location of 'bet' is hardcoded in the app for three locations
> (/usr/bin/bet, /usr/local/fsl/bin/bet, /usr/local/fsl/bin/bet_8UI).
> Installing FSL from neuro-repos drops it into /usr/lib/fsl/4.1/bin/bet,
> although the location set by /etc/fsl/fsl.sh is /usr/share/fsl/4.1
> (symlinked back to /usr/lib/fsl/4.1)
> and unfortunately, none of the three (presumably) hardcoded locations in
> mricron is thus correct.
>
> The ~/.mricron/mricron.ini contains a line for the location of FSLDIR, but
> this seems not to be used, or only _after_ 'bet' (the wrapper script) is
> found in the hardwired location, it seems the FSLDIR dir is used to hold tabs
> on bet2, the actual extraction tool.
> So setting this location to
> FSLDIR=FSLDIR=/usr/share/fsl/4.1
> does lead to bet2 to be found.
> However, bet2 then bails out with libmeshclass.so not found.
>
> source /etc/fsl/fsl.sh _does_ set LD_LIBRARY_PATH=/usr/lib/fsl/4.1 but that
> does not get picked up.
>
>
> To remedy or work around, i
>
> ## FOR ADMIN
> #make the hardcoded bet found:
> mkdir /usr/local/fsl
> cd /usr/local/fsl
> ln -s /usr/share/fsl/4.1/bin
>
> #have bet2 pick up the library
> echo "/usr/lib/fsl/4.1" > /etc/ld.so.conf.d/fsl.conf
> ldconfig
>
> ## FOR USERS
> #edit ~/.mricron/mricron.ini to feed proper FSL location to mricron
> # change FSLDIR (under [STR]) to
> FSLDIR=FSLDIR=/usr/share/fsl/4.1
>
>
> At this point the extraction seems to work.
>
>
> I am not sure if it is only mricron (remove hardcoded line to read the FSLDIR
> location from the mricron.ini file)
> or also FSL (not finding libs after sourcing /etc/fsl/fsl.sh)
> being in need of a change when used from the debian-repos.
--- End Message ---
--- Begin Message ---
Source: mricron
Source-Version: 0.20101102.1~dfsg.1-2
We believe that the bug you reported is fixed in the latest version of
mricron, which is due to be installed in the Debian FTP archive:
mricron-data_0.20101102.1~dfsg.1-2_all.deb
to main/m/mricron/mricron-data_0.20101102.1~dfsg.1-2_all.deb
mricron-doc_0.20101102.1~dfsg.1-2_all.deb
to main/m/mricron/mricron-doc_0.20101102.1~dfsg.1-2_all.deb
mricron_0.20101102.1~dfsg.1-2.debian.tar.gz
to main/m/mricron/mricron_0.20101102.1~dfsg.1-2.debian.tar.gz
mricron_0.20101102.1~dfsg.1-2.dsc
to main/m/mricron/mricron_0.20101102.1~dfsg.1-2.dsc
mricron_0.20101102.1~dfsg.1-2_amd64.deb
to main/m/mricron/mricron_0.20101102.1~dfsg.1-2_amd64.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael Hanke <[email protected]> (supplier of updated mricron package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Wed, 02 Feb 2011 16:18:59 -0500
Source: mricron
Binary: mricron mricron-data mricron-doc
Architecture: source amd64 all
Version: 0.20101102.1~dfsg.1-2
Distribution: unstable
Urgency: low
Maintainer: NeuroDebian Team <[email protected]>
Changed-By: Michael Hanke <[email protected]>
Description:
mricron - magnetic resonance image conversion, viewing and analysis
mricron-data - data files for MRIcron
mricron-doc - data files for MRIcron
Closes: 611374
Changes:
mricron (0.20101102.1~dfsg.1-2) unstable; urgency=low
.
* Change maintainer email.
* Add 'fsl' as a suggested package.
* Add patch to make mricron work with Debian's FSL setup (to call BET for
skull-stripping). Also call mricron via a wrapper that automatically
sources the FSL configuration file on startup. Closes: #611374
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