Thanks Ziad. This looks like it will be helpful, but I don't think that it will completely solve the problem. It appears from reading your documentation that 3dTalign will morph a dataset so that it fits onto another one, which is the first step. I presume this will yield a result similar to that using nudge, but with the ability to morph the data in addition to shift and rotate it.
This seems like it will solve the first problem - aligning the two datasets. Will this work for two anatomical sets as well (my first question)?
The second problem is, when I then go into AFNI, I need to be able to find the location in Talairach space corresponding to a given voxel coordinate from the initial input data. You mention that this 'is taken care of internally', but that's just the problem. I want to be able to explicitly specify a voxel coordinate from the functional data (in pre-transform coordinates), and find out what it's Talairach coordinates are post-transform. This isn't the normal procedure (which is to do the transformation, and then just forget about the original voxel-based coordinate frame).


Thanks,

Christopher