David,
actually, I think this should work with an explicit mask. Did you make
sure that your mask is really binary? If you use e.g. segmentation output
as a mask, then there will be many voxels with near-zero values, which
still will be included in your mask. Only exactly-zero values will be
excluded.
Yours,
Volkmar
On Wed, 3 May 2006, Kareken, David A. wrote:
> For fMRI, I have previously used two methods to change the default mask
> in both spm99 (code supplied by Karl:
> http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind99&L=SPM&P=R151710&I=-3)
> and spm2 ('specmask' code done by Marco Wilke:
> http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind04&L=SPM&P=R238603&I=-3)
> so that the volume analyzed corresponds to a gray matter volume, rather
> than the thresholded intensity mask that spm calculates by default
> (i.e., including areas in which there is some sinus artifact).
>
> However, we can't find how to do that in spm5. Changing the explicit
> mask doesn't seem to really correct the problem, as that appears simply
> to be a union between spm5's default mask and the explicit mask.
>
> Could someone kindly help with this problem? Please cc me directly, if
> you would.
>
> Thanks,
> David K
>
> David A. Kareken, Ph.D., ABPP/ABCN
> Board Certified Neuropsychologist
> Associate Professor & Director of Neuropsychology
> Department of Neurology
> 541 Clinical Drive (CL-299)
> Indiana University School of Medicine
> Indianapolis, IN 46202
> Tel: 317 274-7327
> Fax: 317 274-1337
>
>
>
--
Volkmar Glauche
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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
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