[Neurodebian-users] Seg fault with atlasquery
Jonathan Brooks
Jon.Brooks at bristol.ac.uk
Thu Jan 9 15:27:58 UTC 2014
Here you go:
$ sudo dpkg -l fsl*atlas\*
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Description
+++-==============-==============-============================================
ii fsl-atlases 5.0.5-1 FSL's MNI152 standard space stereotaxic brai
ii fsl-bangor-cer 5.0.5-1 probabilistic atlas of the human cerebellum
ii fsl-harvard-ox 5.0.5-1 probabilistic atlas of human cortical brain
ii fsl-harvard-ox 5.0.5-1 probabilistic atlas of human cortical and su
ii fsl-jhu-dti-wh 5.0.5-1 human brain white-matter atlas
ii fsl-juelich-hi 5.0.5-1 brain atlas based on cyto- and myelo-archite
ii fsl-mni-struct 5.0.5-1 hand-segmented single-subject human brain at
ii fsl-oxford-str 5.0.5-1 probabilistic atlas of the human brain's sub
ii fsl-oxford-tha 5.0.5-1 probabilistic brain atlas of thalamic white-
ii fsl-subthalami 5.0.5-1 probabilistic subthalamic nucleus atlas
ii fsl-talairach- 5.0.5-1 structural anatomy labels of the Talairach a
Debugging info:
$ gdb --args atlasquery --dumpatlases
GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04
Copyright (C) 2012 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
For bug reporting instructions, please see:
<http://bugs.launchpad.net/gdb-linaro/>...
Reading symbols from /usr/lib/fsl/5.0/atlasquery...(no debugging symbols found)...done.
(gdb) r
Starting program: /usr/lib/fsl/5.0/atlasquery --dumpatlases
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
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 Cortical Structural Atlas (Lateralized)
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
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff5825e18 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
(gdb) bt
#0 0x00007ffff5825e18 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#1 0x00007ffff5826b89 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#2 0x00007ffff5375e0f in ?? () from /lib/x86_64-linux-gnu/libz.so.1
#3 0x00007ffff775f344 in Xznzclose () from /usr/lib/libznz.so.2
#4 0x0000000000482a86 in FslClose ()
#5 0x000000000044c2a6 in Image::~Image() ()
#6 0x000000000044c3e9 in Image::~Image() ()
#7 0x000000000042ee5e in Atlas::~Atlas() ()
#8 0x00000000004318f0 in LabelAtlas::~LabelAtlas() ()
#9 0x0000000000431e91 in std::_Rb_tree<std::string, std::pair<std::string const, boost::shared_ptr<Atlas> >, std::_Select1st<std::pair<std::string const, boost::shared_ptr<Atlas> > >, std::less<std::string>, std::allocator<std::pair<std::string const, boost::shared_ptr<Atlas> > > >::_M_erase(std::_Rb_tree_node<std::pair<std::string const, boost::shared_ptr<Atlas> > >*) ()
#10 0x0000000000431e6d in std::_Rb_tree<std::string, std::pair<std::string const, boost::shared_ptr<Atlas> >, std::_Select1st<std::pair<std::string const, boost::shared_ptr<Atlas> > >, std::less<std::string>, std::allocator<std::pair<std::string const, boost::shared_ptr<Atlas> > > >::_M_erase(std::_Rb_tree_node<std::pair<std::string const, boost::shared_ptr<Atlas> > >*) ()
#11 0x0000000000431e6d in std::_Rb_tree<std::string, std::pair<std::string const, boost::shared_ptr<Atlas> >, std::_Select1st<std::pair<std::string const, boost::shared_ptr<Atlas> > >, std::less<std::string>, std::allocator<std::pair<std::string const, boost::shared_ptr<Atlas> > > >::_M_erase(std::_Rb_tree_node<std::pa---Type <return> to continue, or q <return> to quit---
ir<std::string const, boost::shared_ptr<Atlas> > >*) ()
#12 0x0000000000431e6d in std::_Rb_tree<std::string, std::pair<std::string const, boost::shared_ptr<Atlas> >, std::_Select1st<std::pair<std::string const, boost::shared_ptr<Atlas> > >, std::less<std::string>, std::allocator<std::pair<std::string const, boost::shared_ptr<Atlas> > > >::_M_erase(std::_Rb_tree_node<std::pair<std::string const, boost::shared_ptr<Atlas> > >*) ()
#13 0x0000000000431e6d in std::_Rb_tree<std::string, std::pair<std::string const, boost::shared_ptr<Atlas> >, std::_Select1st<std::pair<std::string const, boost::shared_ptr<Atlas> > >, std::less<std::string>, std::allocator<std::pair<std::string const, boost::shared_ptr<Atlas> > > >::_M_erase(std::_Rb_tree_node<std::pair<std::string const, boost::shared_ptr<Atlas> > >*) ()
#14 0x0000000000431e6d in std::_Rb_tree<std::string, std::pair<std::string const, boost::shared_ptr<Atlas> >, std::_Select1st<std::pair<std::string const, boost::shared_ptr<Atlas> > >, std::less<std::string>, std::allocator<std::pair<std::string const, boost::shared_ptr<Atlas> > > >::_M_erase(std::_Rb_tree_node<std::pair<std::string const, boost::shared_ptr<Atlas> > >*) ()
#15 0x00007ffff57e2901 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#16 0x00007ffff57e2985 in exit () from /lib/x86_64-linux-gnu/libc.so.6
#17 0x00007ffff57c8774 in __libc_start_main ()
from /lib/x86_64-linux-gnu/libc.so.6
#18 0x0000000000428641 in _start ()
(gdb) quit
A debugging session is active.
Inferior 1 [process 20641] will be killed.
Quit anyway? (y or n) y
Does that help?
Cheers, Jon
On 9 Jan 2014, at 14:12, Yaroslav Halchenko <debian at onerussian.com> wrote:
> I am yet to check on Ubuntu 12.04, seems to work fine on my Debian
> jessie/sid (see below). Could you list also which atlases you have?
>
> $> dpkg -l fsl*atlas\*
>
> ?
>
> and the next thing would be to see if anything useful would come out of running
>
> gdb --args atlasquery --dumpatlases
>
> then "r<enter>" and whenever crashes "bt<enter>"
>
>
>
> $> 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 Cortical Structural Atlas (Lateralized)
> Harvard-Oxford Subcortical Structural Atlas
> JHU ICBM-DTI-81 White-Matter Labels
> JHU White-Matter Tractography Atlas
> Juelich Histological Atlas
> MNI Structural Atlas
> NeuroSynth (http://neurosynth.org) 100 top terms (posterior_z)
> NeuroSynth (http://neurosynth.org) 100 top terms (prior_z)
> NeuroSynth (http://neurosynth.org) all 525 terms (posterior_z)
> NeuroSynth (http://neurosynth.org) all 525 terms (prior_z)
> 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
>
> $> apt-cache policy fsl-5.0-core
> fsl-5.0-core:
> Installed: 5.0.6-1~nd80+1
> Candidate: 5.0.6-1~nd80+1
> Version table:
> *** 5.0.6-1~nd80+1 0
> 400 http://neuro.debian.net/debian/ jessie/non-free amd64 Packages
> 100 /var/lib/dpkg/status
>
>
> On Thu, 09 Jan 2014, Jonathan Brooks wrote:
>
>> Sorry - I don't think our system allows core files to be written…. there's nothing obvious being created. Unless I'm looking in the wrong place.
>
>> The weird thing is that presumably this same tool gets used to provide atlas information within fslview - which is working fine.
>
>> Cheers, Jon
>
>> On 9 Jan 2014, at 11:10, "Yury V. Zaytsev" <yury at shurup.com> wrote:
>
>>> On Thu, 2014-01-09 at 11:02 +0000, Jonathan Brooks wrote:
>
>>>> I'm not a programmer, so you may have to give me some help with
>>>> debugging. I wouldn't know where to begin with the output from gdb.
>
>>> I think that the first step would be to post it to the list, so that
>>> others can see it :-) Then, someone familiar with source code can have a
>>> look at it and suggest additional tests to narrow down the problem.
>
>>> --
>>> Sincerely yours,
>>> Yury V. Zaytsev
> --
> Yaroslav O. Halchenko, Ph.D.
> 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
>
> _______________________________________________
> Neurodebian-users mailing list
> Neurodebian-users at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
--
Jonathan Brooks (PhD) - Senior Research Fellow
CRiCBristol, University of Bristol, St Michael's Hill, Bristol, UK
T: +44(0)117-342-1512 W: http://www.cricbristol.ac.uk
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