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Thanks for the reply! I tried the --vol-geom orig.mgz option but to no avail.
Small update: I inspected the metadata on the surface files using mris_info and discovered that the ctr property was different between the CAT generated surface and the pial surface that was produced from recon-all, while all the other transforms where the same.
So I figured the difference in the ctr should be compensated by a translation.
To do that, I first created a CAT2FS.fslmat transform of the form:
1 0 0 (CAT.ctr(1)-FS.ctr(1)) 0 1 0 (CAT.ctr(3)-FS.ctr(3)) 0 0 0 (CAT.ctr(2)-FS.ctr(2)) 0 0 0 1
(NOTE: Im sure the order of the translation portion of the matrix has something to do with the orientation convention but I couldnt be bothered to dig deeper - I got this by trial and error)
and then converted it to LTA using lta_convert:
lta_convert --infsl CAT2FS.fslmat --outlta CAT2FS.lta --src orig.mgz --trg orig.mgz
and then applied this transformation using mris_transform:
mris_transform ?h.CAT CAT2FS.lta ?h.CATreg
sure enough when I load CATreg on tkregister2 I see everything perfectly aligned, but after doing mri_vol2surf the surface overlay is still messed up in Freeview. Any suggestions?
Thanks in advance for the help!
Ricardo
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