Arch Linux User Repository

Oh geez my bad, yes that did it @keiichiiownsu12. Thanks so much!

@liamtimms the first atlas tar.gz file I linked is ~134 M uncompressed. Might be better to include as a separate package. However, things get a little dicey, since the atlas_latest.tar.gz file does not contain all atlases included in the normal binary package. and unfortunately afni doesn't exactly say which file is preferred...I'll do some more digging if you like me to find out.

@kcdad have you added afni to your path? if you type export PATH=$PATH:/opt/afni, are you able to run the afni command?

I'm sorry, I must be doing something obviously wrong. But after I install this, I cannot get afni to start (afni is not seen as a command). I tried to follow steps on the afni website seen on other installations (installed R, for example) but it is not clear to me what else I need to do in order to get afni to be a command and get the program to start. Thanks for the help.

@keiichiiownsu12 cheers, thanks. Do you think it would make more sense to try to include these in the default install from this AUR PKGBUILD or in a separate PKGBUILD? How much disk space are they taking after install (and unpacking?) on your machine?

For reference, here is the Neurodebian package I mentioned: https://neuro.debian.net/pkgs/afni-atlases.html?highlight=afni

The Arch "KISS" approach seems to imply these should probably be included here rather than separated out but if they end up being too massive it might make sense to keep them separate.

REALLY wish they'd make this easier to find...: link to other atlas files

@liamtimms looks like it's much simpler than either of us thought. There is a file called "atlases_latest", found here. After the files are extracted, if one places them in /opt/afni (or whichever location afni binaries are stored), the atlases are immediately available for use.

@keiichownsu12 I made a PKGBUILD for python-datalad if you want to try to testing it with that afni_data repo.

hi @keiichiiownsu12 I'm actually not sure as I'm mostly using FSL for atlas fitting. There might be a flag as you suggest but it's not obvious from the documentation. You could try packaging a binary version of it and sharing it on the AUR, it seems like the binaries include the atlases based on the AFNI site.

Poking around a little I did just find this: https://github.com/afni/afni_atlases but I'm not sure why they have it "archived." It might be a good idea to check upstream to see what they recommend. If you can find out the best way to do it with that, I'd be happy to include an atlas download step in this PKGBUILD or you could make a separate AUR entry for the atlases (I think Neurodebian does this).

edit: looks like they have them over here now https://github.com/afni/afni_data it uses DataLad which we definitely should package for Arch if it hasn't been yet. Maybe that's the right place to start.

How might I go about installing some of the default atlases afni is shipped with? E.g. the Talairach daemon. Is it a flag I need to set in the Makefile? Can I just download the atlas from the afni website and drop them into /opt/afni?