I am confused by an analysis where applying an explicit mask seems to
change my uncorrected statistics. To explain fully: I did my first
level analysis with unsmoothed data, and then smoothed the resulting
betas. My smoothed betas for the second level were completely
unmasked - non-zero values filling the whole bounding box, so when I
did the second level analysis I applied an explict mask shaped like
the whole brain. And I got some reasonable activations in the
expected areas. Then I decided my first choice of explicit mask was
not great and applied a slightly different one - about 2 voxels
smaller all over, with quite a lot less cerebellum. I expected my
uncorrected stats for cortical areas to be identical under both masks,
because the mask is identical at this point. But it seems this isn't
the case - all my F values have got a little smaller with the bigger
mask and areas which used to be significant (even ones deep in a
sulcus and nowhere near the changes in the mask) are now subthreshold.
Looking at my spm outputs, there are small differences in smoothness
and larger differences in search vol and resels between the analyses:
mask 1: FWHM 12.3, 12.6, 11.7 mm, search vol 226850 voxels, 932.3 resels
mask 2: FWHM 12.3, 12.6, 11.8 mm, search vol 195379 voxels, 790.3 resels
Can anyone tell me what is causing my uncorrected stats to change?
And how should I make a principled decision about what mask to use?
Thank you in advance,
Antonia.
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