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SPM  April 2008

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Subject:

Re: defaults & spm_jobman

From:

Volkmar Glauche <[log in to unmask]>

Reply-To:

Volkmar Glauche <[log in to unmask]>

Date:

Tue, 8 Apr 2008 19:55:02 +0200

Content-Type:

text/plain

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text/plain (75 lines)

Dear Bas,

you are probably right, this should go into a configuration option for
the job manager. The defaults.mask.thresh and some other options are
currently bypassing SPM5 job management completely. A workaround would
be to implement study specific spm_defaults.m files.

Volkmar

Am Dienstag, den 08.04.2008, 16:56 +0200 schrieb Neggers, S.F.W.:
> Dear List,
>  
> in spm_defaults.m, one can change settings for creating a mask of the
> brain (to exclude analysis of out of brain voxels) using
> defaults.mask.thresh, which defaults to 0.8. For quite a few analyses,
> I need lower values. This is especially when using parallel imaging
> (SENSE), that leads to pretty strong intensity gradients in an image,
> leading to masking out of some in-brain voxels when using 0.8.
>  
> However, what I'm looking for is an option to set this masking default
> (and, for that matter, any other default setting from spm_defaults) in
> the job-manager menu, for use with spm_jobman('run',myjobs). Any other
> method not needing permanent alterations of the spm5 code would also
> be worthwile. I looked for it but couldn't locate it in the
> jobmanager.
>  
> That would be much more practical than changing spm_defaults.m every
> time, and would allow logging of what was actually done. Besides, we
> use one central SPM5 version for the whole group, and changing
> spm_defaults.m for one study would change it for all users, where I
> would like to change it per study depending on the acquisition
> technique used.
>  
> In spm2 one could symply use
>  
> global defaults
> defaults.mask.thresh=<something else>;
>  
> after launching spm2, and the altered threshold would be used. 
> In spm5, I found that spm_defaults is called every time a model is
> specified or estimated, so the above doesn't work anymore.
>  
> Any suggestions?
>  
> Kind regards,
>  
> Bas
>  
>  
> --------------------------------------------------
> Dr. S.F.W. Neggers
> Division of Brain Research
> Rudolf Magnus Institute for Neuroscience
> Utrecht University Medical Center
> 
> Visiting : Heidelberglaan 100, 3584 CX Utrecht
>            Room B.01.1.03
> Mail     : Huispost B.01.206, P.O. Box 85500
>            3508 GA Utrecht, the Netherlands
> Tel      : +31 (0)88 7559609
> Fax      : +31 (0)88 7555443
> E-mail   : [log in to unmask]
> Web      : http://www.fmri.nl/people/bas.html
> --------------------------------------------------
> 
> 
>  
-- 
Volkmar Glauche
-
Department of Neurology         [log in to unmask]
Universitaetsklinikum Freiburg  Phone   49(0)761-270-5331
Breisacher Str. 64              Fax     49(0)761-270-5416
79106 Freiburg                  http://fbi.uniklinik-freiburg.de/

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