Hi Doug,
Thanks! I was wondering: when I have selected "Calculate Identity Matrix" to overly functional data on the fly in the tksurfer gui before, it seems to align it perfectly to the freesurfer anatomical. Is there a way to output the matrix that it's using as a register.dat file? I was trying last week to make the file using tkregister2 and for some reason it always came out misaligned (that's why I started just using the gui). mri_vol2surf is working to make surface overlays, but they don't line up right, presumably because it's using the old register.dat file from tkregister2.
mri_vol2surf --src 003/bold/03.trim_time.tval+orig.BRIK --src_type afni --srcreg register.dat --hemi lh --projfrac .3 --out trim_time.tval.surf.5 --out_type paint
Emily