I am using afni_proc.py for some pre-processing. I added -AddEdge as an option as part of my align_epi_anat block.
This has successfully generated a folder of edge images, but when it has run and I cd into the AddEdge folder, when I try to run @AddEdge -auto it throws up a bunch of different overlaid images one after the other, all disappearing quickly, leaving only my original anatomical image as the background with cyan edges, and a big block cyan blob (not aligned correctly) as my epi. My epi is a partial coverage slab, which is why they aren’t aligned, but not sure what else is going on for this review script to be acting strangely.
When I view the files separately by opening afni on it’s own and setting the overlay and underlay, this works ok, but I can’t work out how to colour the underlay, overlay and overlap differently so I can actually see how well aligned the images are (currently are greyscale).
Any help would be appreciated, thank you!
code (in case it is useful)
afni_proc.py -subj_id $subj