confused by exclusion mask when aligning to template

AFNI Message Board
1

AFNI version info (afni -ver):
Precompiled binary macos_10.12_local: Dec 6 2024 (Version AFNI_24.3.08 'Elagabalus')

I am nonlinearly aligning a subject's T1 (source) to the NMT template (base). I am using 3dQwarp with -allineate. There is an unusual feature in the subject's T1 that (I think) messes up with the alignment.

So I'd like to exclude that feature.

I drew an exclusion mask on the subject's T1. But the mask should be in base volume coordinates... how do I deal with it? Should I warp NMT to the subject making the subject my base, save the linear & non-linear transform, and then invert them and apply to the subject T1?

2

Swapping the source input and base datasets seems reasonable. You can save the inverse warp with the -iwarp option. Another solution is simply to zero out the mask on input and apply the warp to the T1. The solutions will be different.

3

Thank you.

Just to be sure, for the second solution do you mean making the input (i.e. the subject T1) zero wherever the mask is non-zero? If yes, wouldn't it "attract" this region to dark areas of the template which are closer to 0 than brighter areas?

This probably also tells you that I don't know how emask works internally during the alignment. I imagined that conceptually it replaces the masked input with NaNs or something like that and the cost function is not computed over the masked region. And, for non-linear alignment, the warp over that non-existent region is extrapolated from the neighboring, existent regions. Is it any close to waht's happening?

4

Yes, that's what I meant. The exclusion mask works by adjusting the weighting of the costs to zero within the mask on the base dataset. 3dAllineate's help has a bit more description:

-emask ee = This option lets you specify a mask of voxels to EXCLUDE from
the analysis. The voxels where the dataset 'ee' is nonzero
will not be included (i.e., their weights will be set to zero).
* Like all the weight options, it applies in the base image
coordinate system.