So, back to the bench for me, and I see all the updates to AFNI. I originally old-schooled it with aligning MP-RAGE structurals to the 3d+time dataset by eyeballing it. Then I'd eyeball the MP-RAGE structure landmarks, to create the +acpc and +tlrc versions of the structural. When visualizing activation maps in native space, I could just toggle "Talairach View" in the AFNI GUI and the activation map would be pulled into Tlrc space along with the hi-res structural overlay to make the pretty pictures for manuscripts. I assume this was because of the "Warp Olay on demand worked."

Now, I used:

align_epi_anat.py -anat structural+orig -epi XYCPTvr+orig -epi_base 700

in order to move the structural to have it conform (in native space) to the functional..

This looked like a nice co-registration to me.

then I used

@auto_tlrc -base TT_avg152T1+tlrc -input structural_al+orig -ok_notice -dxyz 1.0

And got a nice warping of the structural into Tlrc space to visualize.

However, when I look at the activation map atop the structural in native space, and then try to warp the whole shebang into trlc space, the overlay gets booted and left behind.

What happened, and how do I get back to the old days where my statistical maps would go into trlc space for the ride?

Jim