[Neurodebian-users] Seg fault with atlasquery

[Yaroslav Halchenko]

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