Hi Jim,

AFNI's manual landmarking method performs the transformation of datasets to Talairach-Tourneaux stereotaxic coordinates. The @auto_tlrc script doesn't use the TT brain. Instead, it provides you, the user, with 3 possible templates with which to warp/standardize your datasets: (1) N27 brain, a.k.a. "Colin brain", (2) icbm452, or (3)mni152. These templates differ from each other (e.g., they're different sizes) and they differ from the TT brain. Also, the Anterior Commisure center is no longer at 0,0,0 (but it IS for the manual method) and the size of the brain box is that of the template you use. For these reasons, it's recommended you select one template/method for your data sample and remain consistent.

People often use the term "Talairach" generically, so even if they've used, for example, the icbm 452 template, they still refer to their standardized volumes as being "Taliarached", but that's not entirely accurate. I think this leads to some confusion, so keep in mind that the @auto_tlrc script in AFNI uses templates other than the TT-atlas.

Hope this helps,
Peggy