[Neurodebian-users] FSL atlasquery

[Yaroslav Halchenko]

ok -- no need for locales -- replicated in a clean precise chroot:

# atlasquery --dumpatlases
Cerebellar Atlas in MNI152 space after normalization with FLIRT
Cerebellar Atlas in MNI152 space after normalization with FNIRT
Harvard-Oxford Cortical Structural Atlas
Harvard-Oxford Subcortical Structural Atlas
JHU ICBM-DTI-81 White-Matter Labels
JHU White-Matter Tractography Atlas
Juelich Histological Atlas
MNI Structural Atlas
Oxford Thalamic Connectivity Probability Atlas
Oxford-Imanova Striatal Connectivity Atlas 3 sub-regions
Oxford-Imanova Striatal Connectivity Atlas 7 sub-regions
Oxford-Imanova Striatal Structural Atlas
Subthalamic Nucleus Atlas
Talairach Daemon Labels
Segmentation fault

valgrind (running as simple as 'sudo apt-get install valgrind; valgrind
atlasquery --dumpatlases' happens you need this in future) gives gory
details:

==1397== Invalid read of size 4
==1397==    at 0x663D424: ??? (in /usr/lib/x86_64-linux-gnu/libQtCore.so.4.8.1)
==1397==    by 0x67553AA: QObjectPrivate::~QObjectPrivate() (in /usr/lib/x86_64-linux-gnu/libQtCore.so.4.8.1)
==1397==    by 0x6706CA6: ??? (in /usr/lib/x86_64-linux-gnu/libQtCore.so.4.8.1)
==1397==    by 0x6706E98: ??? (in /usr/lib/x86_64-linux-gnu/libQtCore.so.4.8.1)
==1397==    by 0x6757BCF: QObject::~QObject() (in /usr/lib/x86_64-linux-gnu/libQtCore.so.4.8.1)
==1397==    by 0x449D4F: Preferences::~Preferences() (in /usr/bin/atlasquery)
==1397==    by 0x449B18: boost::shared_ptr<Preferences>::~shared_ptr() (in /usr/bin/atlasquery)
==1397==    by 0x72E3900: __run_exit_handlers (exit.c:78)
==1397==    by 0x72E3984: exit (exit.c:100)
==1397==    by 0x72C9773: (below main) (libc-start.c:258)
==1397==  Address 0xab860e0 is 0 bytes inside a block of size 104 free'd
==1397==    at 0x4C2A4BC: operator delete(void*) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==1397==    by 0x674376D: ??? (in /usr/lib/x86_64-linux-gnu/libQtCore.so.4.8.1)
==1397==    by 0x72E3900: __run_exit_handlers (exit.c:78)
==1397==    by 0x72E3984: exit (exit.c:100)
==1397==    by 0x72C9773: (below main) (libc-start.c:258)

so I suspect it is a bug in Qt 4 as provided on Ubuntu precise -- not sure what
will be our next step -- may be Michael would like to look deeper (I left that
chroot available under my screen on neurohydra).  (just a thought outloud:
there is a reason why generally recommend using Debian and not its
derivatives, where we have less control over releases/bugs etc)

On Mon, 11 Mar 2013, Yaroslav Halchenko wrote:


> On Mon, 11 Mar 2013, Bertram Walter wrote:

> > since I installed the new fslview, atlasquery crashes wit a
> > segmentation fault.

> sorry

> as you might guess your report is not sufficient ATM to reproduce or
> diagnose the problem.  Provide

> 1. information on the system (release, architecture)
> 2. sample cmdline lead to segfault

> since "works for me":

> $> atlasquery -a "Harvard-Oxford Cortical Structural Atlas" -c 30,30,20
> <b>Harvard-Oxford Cortical Structural Atlas</b><br>1% Middle Frontal Gyrus, 1% Frontal Pole
-- 
Yaroslav O. Halchenko
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate,     Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik