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

[Bertram Walter]

> 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
-- 
Dr. Bertram Walter
Bender Institute of Neuroimaging
University of Giessen
Otto-Behaghel-Str. 10H
35394 Giessen
Germany
Phone +49 (641) 99-26307
    or +49 (641) 99-26331 (Secretary)
Fax   +49 (641) 99-26309
www.bion.de