Dear AFNI developers and experts,
I encountered an issue that I had not quite expected in the behaviour of 3dresample. I found a way around this (using another tool) but wanted to post it here anyway in case other people experience the same issue.
Essentially, I have a functional image (pre.nii.gz) at an oblique angle that I want to upsample.
So I use:

3dresample -input pre.nii.gz -prefix pre_resampled.nii.gz -dxyz 1 1 1

I think the pre_resampled.nii.gz output somehow has a different oblique angle. Indeed, when I load pre as underlay and pre_resampled as overlay, AFNI tells me: "The underlay/overlay pair of datasets (...) have oblique angle difference of 22.60 degrees." When I click away that message the images do show up in alignment in AFNI. However, other tools disagree. For example fsleyes shows the two images as being wildly out of alignment (see attached figure). Also, when I do further processing with this such as applying transforms with this resampled image as a reference (using antsApplyTransform) the result is images that are cut.

I suppose this may somehow be the intended way for 3dresample to work, but for me it was unexpected, so I wanted to mention it here.
Thanks!