Hi there,

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!

Harriet

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code (in case it is useful)

afni_proc.py -subj_id $subj \
-blocks align \
-dsets $data_dir/P007_FR_RUN* \
-tcat_remove_first_trs 0 \
-copy_anat $data_dir/FR_uniden_avg \
-anat_has_skull yes \
-align_opts_aea \
-deoblique on \
-ginormous_move \
-partial_coverage \
-AddEdge \
-check_flip



Edited 1 time(s). Last edit at 03/04/2021 01:05AM by hdempseyjones.