Hi Rachel,
Did you ever get any replies, or get anywhere with this?
> Essentially my concern is that the group activations (as shown by an SPMT
> image for one particular contrast) do not line up with the outer edge of
> cortex in my averaged wmT1 or the SPM single-subject canonical template.
> This is the case for all group T images.
>
> Individual subject normalisation was accurate as verified visually using
> check reg - both individual structural and mean functional images match
> the T1 template and wmT1 accurately. The problem seems to arise when I do
> a group analysis.
What about check reg of the individual con images that you are
entering into the group analysis (compared to the template), how do
they look? Also, check the individual mask images, and the group-wise
mask image, that get written to the results directories.
You might want to try creating the intersection of all individual mask
images, to see if it is misalignment that is causing the problem. You
should be able to do this with imcalc, using the dmtx flag, and an
expression something like 'all(X>0)', then compare that result to both
the template, and the group-analysis mask.
Hope that helps,
Ged.
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