Hi Kosuke,
Sorry for the slow reply,
> When I perform a one-sample t-test on a certain set
> of con images without absolute threshold masking, I get
> FWHM: [0.0000 0.1336 0.0000] (pixels).
> There are no NaNs in the first level contrasts. Implicit mask is
> specified at the second level, but I don't think it makes a difference for
> contrast images that have float precision. So, if I understand
> correctly, the net effect is no masking at all (except for voxels that
> have constant values across subjects).
I agree.
> Then I thought I should try specifying an explicit mask in the form of a
> mask image that had zeros for out-of-brain voxels. It seems to work, as
> the smoothness estimate is now more reasonable:
> FWHM: [4.2832 4.7114 4.2297] (pixels).
> I think this is a better solution than thresholding, and plan to go on
> with this method of analysis. Please let me know if there is anything
> wrong with this approach.
I agree that explicit masking sounds much safer, and should be an
entirely reasonable thing to do. However, it might be wise to double
check the first level results, to see if there is an obvious reason
for the poor smoothness estimates. Perhaps this is a common problem
with second level analysis (any fMRI folk want to comment?), but if
not, it might be a symptom of a problem that you should fix rather
than avoid...
Best,
Ged.
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