Dear Marris,
Based on the "regular" shape of the segmented image I guess you look at the raw image and a normalized file from the segmentation step (which seems to have been successful), so obviously, they won't match. You would have to compare the raw image to the c1, c2, c3 and/or the (m)wc1, (m)wc2, (m)wc3 to the tissue probabily maps or templates.
By the way, what did https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;f5c09487.1505 show? A c1 file? The new c1 file should be much better, otherwise the presumable normalised file would look much worse.
If it's not a normalised file, then this would be pretty weird & requires some further inspection. You could send the raw structure to me then.
Best
Helmut
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