Hi,
I am a bit noob on FreeSurfer and coordinate systems. I am wondering if I have the T1.mgz file of FreeSurfer after running recon-all and this is the 256^3 image re-scaled and re-oriented from your orig.mgz file, then how does one define the fsnative (volume RAS) vs surface RAS (tkras in FreeSurfer) in terms of origin? Assume I do no preprocessing on the original scanner nifti.
When I say volume RAS (fsnative), I mean the xyz coordinates obtained from vox2ras. When I say surface RAS (fstkras), I mean the xyz coordinates obtained from vox2tkras.
Is the Volume RAS origin anything special, like the AC? Does FreeSurfer internally try to align it that way?