What I meant to say was that the overlay was still “offset" from the actual volume. See attachment. It is the side view of the CAT 3D surface in grey and in red what should be the qMRI overlay (generated using mri_vol2surf). The yellow arrow represents the offset.

After the ctr change by the previously described method, I ran mri_vol2surf with the --regheader option as suggested initially. Turns out, this option was the responsible for this latest offset. So, after running mri_vol2surf without this option I got the overlay to match the surface perfectly in Freeview.

On 22. Feb 2019, at 14:58, Loucao, Ricardo <r.loucao@fz-juelich.de> wrote:

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