Are the Talairach coordinates from AFNI the same as from SPM?
Not exactly. AFNI tries to follow the 1988 Talairach-Tournoux Atlas as far as possible. This was requested by the FMRI researchers at MCW back in 1994 (when AFNI was born). This is why the program requires you to choose the superior margin of the AC, rather than the center, since that is what the Atlas does. This is why you pick the brain bounding-box points after alignment to the AC-PC axis, since that alignment defines the anterior-posterior, superior-inferior, and right-left axes. This is why 12 sub-volumes are used to define the transformation, rather than using a single affine mapping for the whole brain volume. Most other software, including SPM, does a single affine transform for the entire brain (a simpler alternative), or does a high dimensional nonlinear transformation (a much more complex alternative). A description of how SPM and the MNI software packages do the T-T transformation can be found here. Because they use a different “standard brain” than the Talairach-Tournoux a
