Now that I'm looking at this more, I think I had it wrong initially. The first command on fdt_surface.html is:
tkregister2 --mov $SUBJECTS_DIR/john/mri/orig.mgz --targ $SUBJECTS_DIR/john/mri/rawavg.mgz --regheader --reg junk --fslregout freesurfer2struct.mat --noedit
but isn't that creating struct2freesurfer.mat, and not the other way around? In which case, my previous post suggesting adding an additional inversion step would be incorrect.
Sorry for the confusion.
Cheers,
Ryan
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