[Neurodebian-users] Neurodebian-users Digest, Vol 31, Issue 5

[Yaroslav Halchenko]

and I guess
Speicherzugriffsfehler (Speicherabzug geschrieben)
means "Segfault" in german...

what is the output of running "locale" command? (meanwhile will test in
a clean 12.04 env

On Wed, 13 Mar 2013, Bertram Walter wrote:

> >Message: 1
> >Date: Mon, 11 Mar 2013 08:43:56 -0400
> >From: Yaroslav Halchenko <debian at onerussian.com>
> >To: neurodebian-users at lists.alioth.debian.org
> >Subject: Re: [Neurodebian-users] FSL atlasquery
> >Message-ID: <20130311124356.GS2004 at onerussian.com>
> >Content-Type: text/plain; charset=utf-8


> >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




> Hi,

> Sorry, here's the the information:

> Computer name bion71
> Ubuntu 12.04 (precise) (64-Bit)
> kernel Linux 3.2.0-38-generic

> Hardware
> RAM 15,6 GiB
> Processor: Intel Core i7 CPU 860 @ 2.80 GHz x 8

> Installed fsl 5.0.2-4~nd12.04+1

> command:
> bion-u at bion71:~$ atlasquery -a "Harvard-Oxford Cortical Structural
> Atlas" -c 30,30,20
> result:
> <b>Harvard-Oxford Cortical Structural Atlas</b><br>1% Middle Frontal
> Gyrus, 1% Frontal Pole
> Speicherzugriffsfehler (Speicherabzug geschrieben)

> atlasquery --dumpatlasses
> X_OptionError: --dumpatlasses: Option doesn't exist!
> Speicherzugriffsfehler (Speicherabzug geschrieben)

> command:
> bion-u at bion71:~$ atlasquery --dumpatlases
> result:
> 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
> Speicherzugriffsfehler (Speicherabzug geschrieben)

> command:
> bion-u at bion71:~$ atlasquery
> result:
> ***************************************************
> The following COMPULSORY options have not been set:
> 	-a,--atlas	name of atlas to use
> ***************************************************

> Part of FSL (build 4110)
> atlasquery (version 1.0)

> Copyright(c) 2005, University of Oxford
> Dave Flitney

> Usage:
> atlasquery [-a "<atlasname>"] [-m <maskimage>] [-c <X>,<Y>,<Z>]

> Compulsory arguments (You MUST set one or more of):
> 	-a,--atlas	name of atlas to use

> Optional arguments (You may optionally specify one or more of):
> 	-V,--verbose	switch on diagnostic messages
> 	-h,--help	display this message
> 	-m,--mask	a mask image to use during structural lookups
> 	-c	
> 	--dumpatlases	Dump a list of the available atlases


> Speicherzugriffsfehler (Speicherabzug geschrieben)


> This behavior is the same on all our linux machines.

> If I take the 64-bit atlasquery binary from the centos6 distribution
> from fmrib everything runs fine:

> ***************************************************
> The following COMPULSORY options have not been set:
> 	-a,--atlas	name of atlas to use
> ***************************************************

> Part of FSL (build 416)
> atlasquery (version 1.0)

> Copyright(c) 2005, University of Oxford
> Dave Flitney

> Usage:
> atlasquery [-a "<atlasname>"] [-m <maskimage>] [-c <X>,<Y>,<Z>]

> Compulsory arguments (You MUST set one or more of):
> 	-a,--atlas	name of atlas to use

> Optional arguments (You may optionally specify one or more of):
> 	-V,--verbose	switch on diagnostic messages
> 	-h,--help	display this message
> 	-m,--mask	a mask image to use during structural lookups
> 	-c	
> 	--dumpatlases	Dump a list of the available atlases

> Best regards

> Bertram
-- 
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