Just adding my 2 cents in:
Karsten,
I'm confused as to why you say most of the masking happens during
normalization? Can you explain what you mean?
Asaf,
During 1st level model estimation SPM calculates a mask (saved as
mask.img in the stats directory); this is generally a good brain mask,
and limits the number of voxels that are estimated when fitting the
model. So, I don't think you would gain much by using an explicit
whole brain mask. It probably wouldn't hurt, although you would want
to make sure that, however you calculated your brain mask, you weren't
cutting out any voxels of BOLD signal.
Best regards,
Jonathan
On Thu, Aug 12, 2010 at 9:04 AM, Karsten Specht <[log in to unmask]> wrote:
> Hi Asaf,
>
>>Suppose I don't want to choose or to leave out certain areas in the analysis (i.e., i want to
>>perform a whole brain analysis), is there any point in using this option? >I read in the manual (section 8.8) that it speeds up the estimation process - Will it be wise
>>to use my SPGR image of the whole brain, have I got anything to lose if I do this?
> yes, of course, you can use your own brainmask, but note that most of the masking already happens during the normalisation, not during the estimation of your model.
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