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When trying to use the 2nd AP/PA pair with the first set of scans (e.g., because something bad happened during the first pair, like yawning or errors during acquisition), indexing gets off due to how AFNI renames files within afni_proc.py
Specifically, if you use a SEtargets.txt file like:
2 01 04
3 05 06
because the AP/PA pair acquired between runs 2/3 (blip_for/rev1) is inadequate, you'll end up using blip_for/rev3 to correct runs 1-4, and 4 to correct runs 5-6.
The solution to this isn't obvious right now, except for renaming blip pairs to start at 1 and increase consecutively if an error is found.
The text was updated successfully, but these errors were encountered:
When trying to use the 2nd AP/PA pair with the first set of scans (e.g., because something bad happened during the first pair, like yawning or errors during acquisition), indexing gets off due to how AFNI renames files within afni_proc.py
Specifically, if you use a SEtargets.txt file like:
2 01 04
3 05 06
because the AP/PA pair acquired between runs 2/3 (blip_for/rev1) is inadequate, you'll end up using blip_for/rev3 to correct runs 1-4, and 4 to correct runs 5-6.
The solution to this isn't obvious right now, except for renaming blip pairs to start at 1 and increase consecutively if an error is found.
The text was updated successfully, but these errors were encountered: