Hi Nick,

It does look like there is an LPI/RAI problem here but I am not sure where it is getting introduced. I do use GIFTI versions of FreeSurfer surfaces fine so there has to be something else going on here.

If I understand what is going correctly, if the GIFTI files do not have the affine transform modified to have -1 in the 1st two diagonal elements, then after pressing 't', the contours of the surfaces look flipped in AFNI.

If you use -1 in the 1st two diagonal elements, then contours look fine in AFNI, but rotation in SUMA is messed up.

1- Let us verify what is happening to the Center of Mass Estimate in SUMA:
Start SUMA on the set of GIFTI surfaces without changes to the affine transform, open the surface controller for one hemisphere and click 'more' under the "surface properties" block. Then search for "Center of Mass" and note the value
Repeat on the set of GIFTI surfaces with the changes to the affine transform, what is the new value of the center of mass?

2- Instead of changing the affine transform, can you explicitly flip the x and y coord sign before writing out the GIFTI files? And when you do this, do things work OK?

Hopefully this will get us somewhere good quickly. I am glad you reached the GIFTI route, I was going to propose using it anyway.

cheers
z