Dear Kathy, Volkmar and Christian,
thank you all for these helpful suggestions, I will explore the mentioned
options and post a response to the list which one worked for me or not.
Cheers,
Niels
______________________________________________________
Dr. med. Niels Focke
Dept. of Clin. Neurophysiology
UMG - University Hospital Göttingen
http://www.neurologie.uni-goettingen.de/
-----Ursprüngliche Nachricht-----
Von: Christian Gaser [mailto:[log in to unmask]]
Gesendet: Freitag, 28. Mai 2010 00:35
An: [log in to unmask]; Focke, Niels
Cc: Christian Gaser
Betreff: Re: SPM without display
Dear Niels,
you can try the shell script cg_spm8_batch.sh which is included in VBM8
(http://dbm.neuro.uni-jena.de/vbm8/). With this tool you can call spm batches
(saved as .m) from the command line. However, it is not working for all SPM
batches, even if the matlab batch is called as non_gui.
Regards,
Christian
____________________________________________________________________________
Christian Gaser, Ph.D.
Assistant Professor of Computational Neuroscience
Department of Psychiatry
Friedrich-Schiller-University of Jena
Jahnstrasse 3, D-07743 Jena, Germany
Tel: ++49-3641-934752 Fax: ++49-3641-934755
e-mail: [log in to unmask]
http://dbm.neuro.uni-jena.de
On Thu, 27 May 2010 10:48:10 +0200, Focke, Niels <[log in to unmask]>
wrote:
>Dear Experts,
>
>me are currently trying to run scripted/automated SPM8 processing on a
>cluster engine (SGE, Centos Linux). Principally this is easily done by small
>wrapper scripts that call Matlab with the -r (function) -nodesktop -nosplash
>option. However many SPM functions seem to expect a display to be available
>which is not present in this scenario. Although some steps work with a
simple
>warning that a display is missing ("Warning: Unable to open display."),
>several actually fail, e.g. coregistration :
>
>
>> Failed: 'Coreg: Estimate'
>> Error using ==> set
>> Width and height must be > 0
>> in file "(...)/spm_orthviews.m" (v2947), function "bbox" at line 830
>...
>
>
>Is there a way to suppress the SPM8 output? Or forward the display to
>/dev/null? Anyone tried something similar?
>
>
>Any suggestions are very much appreciated.
>
>
>Niels
>
>
>______________________________________________________
>
>Dr. med. Niels Focke
>Dept. of Clin. Neurophysiology
>UMG - University Hospital G�ttingen
>http://www.neurologie.uni-goettingen.de/
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