@auto_tlrc to overlay +orig ROIs on +tlrc template

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?

If they are already aligned, perhaps just make standard
space versions of them, i.e. copy to new files and run
“3drefit -view tlrc”.

  • rick