Should @animal_warper copy atlas and segmentation followers to the output directory? Help suggests that it should (see below), but I do not see anything like that in the output directory. What am I missing here?
Main datasets ~2~
The following are all contained in the main output directory
+ Template dsets and followers in template space
o TEMPLATE - copy of "-template .." (not abbrev)
o TEMPLATE_MASK - copy of "-skullstrip .." mask (not abbrev)
o ATL_FOLL - copy(s) of "-atlas_followers .." (not abbrev)
o SEG_FOLL - copy(s) of "-seg_followers .." (not abbrev)
o TEMPLATE_FOLL - copy of "-template_followers .." (not abbrev)
Yes, the program should. What version of @animal_warper and AFNI do you have?
… that being said, I see in the code that the atlas followers are copied, and then I put a commented note:
# ----- SHOULD ALL FOLLOWERS BE COPIED HERE AS WELL ???
… because I wasn’t sure if copying all files would lead to too many files being present (something people have commented on).
At the moment, the template, brainmask and atlas followers are all copied over, as well as the “input” (=subject) anatomical. Would it be useful to you to have all the followers copied in?
Precompiled binary linux_ubuntu_16_64: Mar 3 2021 (Version AFNI_21.0.13 'Titus')
For what I am working on now I am fine without copying my followers. I have them listed in a variable and instead of making copies (multiple, because one per subject) I can just use the follower I need via $refseg. (I am modifying MACAQUE_DEMO_REST for my purpose).
I just found what seemed like a discrepancy between documentation and behavior so I wanted to report it so it can be fixed. Or, explained to me why it is not a discrepancy if it was me being dumb and missing something.
Sure, thanks for pointing that out—definitely helpful to find errors in the documentation (but who reads help files anyways, right??).
I think my intention was to copy them all over, perhaps that is the better way to go (I could add a switch for people to not-copy them, if they wanted).