Hi all,

as usual I feel dumb asking these questions because it feels as if I am missing something trivial... but I cannot figure it out myself.

I am using align_epi_anat.py to align an anatomical T2 to an earlier anatomical T1 in the same NHP. The overall goal is to align that T2 to NMT, but I wasn't able to do it directly. So I am using @animal_warper to align the T1 to NHP, and align_epi_anat.py to align T2 to T1, and the plan is to catenate the transforms.

It seems to be working fine, I may have to add a non-linear step after align_epi_anat.py because the brain has changed in some crucial areas, but that's in the future.

At this point I wanted to ask - why my T2 is being cropped by align_epi_anat.py and how can I avoid/control this?

In the image, the top row is the result of align_epi_anat.py, showing aligned T2 in greyscale as OL, the T1 is UL in color The bottom row is the T2 (as greyscale UL) as submitted to alignment. Why is the bottom and especially the front cut off? I placed the cursor on the same feature and the image ends there in the result but there are a couple more anterior slices in the source file.

Can I somehow save that front? I know there is not much there, but still it's a part I am interested in.