Re: [Freesurfer] Confused with Coordinate System in FS

2013-04-07 Thread Bruce Fischl
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

[Freesurfer] Confused with Coordinate System in FS

2013-04-07 Thread ZhiLiangLong
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