Thanks for the reply!

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:

(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