Hi Ziad (aka Godot) -

I think that I've isolated the problem. Here's what we did for the registration, and what I think is going wrong.

We did do an unconventional registration between the SurfVol to the experimental functional data (I can provide reasons later, if necessary). We first aligned the high-resolution structural to the functionals using the Freesurfer (FS) tool tkregister-sess. This produces a register.dat file that is the matrix to align the funtionals to the structurals.

We generated SurfVol and associated surface spec files from the FS high-resolution structurals. To get SurfVol registered with the functional BRIKS, we applied the inverse matrix of register.dat to SurfVol using the FS tool mri_vol2vol. This gave us structurals aligned with the functionals, but not with the surfaces. To get the structurals and surfaces aligned with the functionals, we used 3dvolreg to register SurfVol to the structurals_aligned_with_functionals.

The command for 3dvolreg was essentially this:
3dvolreg -wtrim -clipit -twopass - twodup -rotcom -verbose -coarse 4 3 -maxiter 50 -base structurals_aligned_with_functionals+orig -prefix structural_transform SurfVol

This gave us the desired structural volume that was aligned with the functionals and surfaces.

Then we rechecked our structural_transform to functional data alignment, using the AFNI nudger, then applied 3drotate to the structural_transform, if necessary, to give us structural_transform_nudge.

Upon checking this now, using afni -niml&, followed by suma -spec SurfVol_?h.spec -sv structural_transform_nudge

The program spits out:
"Notice SUMA_Apply_VolReg_Trans:
Found both Volreg and Rotate fields.
Using Volreg field for alignment.

And, I see that the surfaces are NOT aligned with the structurals.

So, the question now is: is this just a viewing issue, or does this indicate that the mapping of the funtionals to the cortical surfaces was not correct because the surfaces were truly not aligned with the structurals.

If the later, do I need to apply 3dvolreg (or &SUMA_AlignToExperiment) to SurfVol (relative to structural_transform_nudge) to get the surfaces aligned with the structurals?

Please set me straight! (And sorry for the long message)

Thanks,
Judith