I have some ROIs that I want to view as an overlay on top of a +tlrc template. I currently can’t because the ROIs are not +tlrc (they are a .nii file) so AFNI switches the underlay every time I try. The ROIs and template are already aligned, but AFNI just doesn’t realize it yet. I ran the following:
@auto_tlrc -base modeltemplate_ns.nii -input Warped_ROIs.nii -no_ss
the output was misaligned (tilted). All I want to do is be able to view the images together, which I believe requires the ROIs to be +tlrc. They do not need to be aligned at all. Is there a better way to accomplish this?