Dear Hankee,
Your problem is that you have not checked your initial results like
I asked you to and like it says to in the documentation!
In particular, under the section "General advice and workflow" it
asks you to check registrations and check segmentations. For two
of your subjects the registrations are wildly wrong. See the image
below and the full slicesdir at:
http://users.fmrib.ox.ac.uk/~mark/files/first_badreg_slicesdir/
You can clearly see that subjects E05 and N06 have failed badly.
This needs to be fixed before attempting to do anything else.
You should be able to fix these by appropriately cropping and/or
reslicing them to axial orientation (see fslswapdim).
Please, please, please always check your results before moving
onto subsequent analyses.
If you have problems getting this to work or getting vertex analysis
to work *after* you've fixed the original segmentations and checked
them appropriately, then feel free to email us again.
Mark
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