[Freesurfer] Confused with Coordinate System in FS

Hi all: I am confused with coordinate systems in FS. I have several questions bellow. 1. when we run recon-all -s subjid -all, Is the individual native space transformed to talairach coordinate system?. when run recon-all -s subjid -qcache, does the talairach system go into MNI syst

[Freesurfer] Fwd: Freesurfer Digest, Vol 109, Issue 21

Hi Doug, Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ? When I first run the script, I got all values and looked the the CC - it looked

Re: [Freesurfer] Confused with Coordinate System in FS

there is pretty extensive documentation on the (always confusing) coordinate systems we use - we do *not* resample into tal coords - all calculations are done in subject native space, after resampling to 256^3, 1mm iso (which we call "conforming" for no very good reason) - The talairach.xfm