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
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> 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/
