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
--------------------------------------------------