Package Details: afni 23.0.01-1

Git Clone URL: https://aur.archlinux.org/afni.git (read-only, click to copy)
Package Base: afni
Description: An open-source environment for processing and displaying functional MRI data
Upstream URL: http://afni.nimh.nih.gov
Licenses: custom
Submitter: crmullins
Maintainer: liamtimms (keiichiiownsu12)
Last Packager: liamtimms
Votes: 1
Popularity: 0.000000
First Submitted: 2016-06-29 01:28 (UTC)
Last Updated: 2023-01-24 21:05 (UTC)

Pinned Comments

liamtimms commented on 2022-05-10 20:27 (UTC)

AFNI releases get tagged with a frequency approaching individual git-commits (sometimes multiple times in one day). I update this package semi-regularly to keep it current but do not update it for every single AFNI release tag to avoid excessive burden on users. Please do not flag this package "out-of-date" without some technical justification. If the constant bleeding edge is required for your use case, I recommend using a -git package or using this PKGBUILD as a base and updating to each release tag yourself.

ptaylor.afni commented on 2022-01-21 15:02 (UTC)

@keiichiiownsu12 :

  • Sure, workflow for reporting ArchLinux-AFNI issues could certainly go in that order (i.e., start this forum). I can also be pinged, too, though packaging questions will likely have to be dealt with by smarter folks...

  • Re. packaging: All the datasets for the distribution should just be in one places now (https://afni.nimh.nih.gov/pub/dist/atlases/atlases_current.tgz), whether you unpack+distribute it (which is what we do with the main distributions) or you ask people to get it separately. So, whatever you decide, hopefully it is simpler now.

Latest Comments

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ptaylor.afni commented on 2022-11-01 20:56 (UTC)

@keiichiiownsu12: I'm glad to hear it works well on your systems. Indeed, this should not occur generally, but only if a particular OS is not connected to the internet or something. In such cases, setting the "AFNI_WEBBY_WAMI = NO" environment variable should solve it. And the other "whereami" functionality should work fine---providing locations to specified atlases on the computer, etc.

keiichiiownsu12 commented on 2022-11-01 19:28 (UTC)

@ptaylor.afni and @nikinbaidar: whereami works fine on vanilla X11 GNOME and KDE, so I do not think the server is necessarily the issue.

@nikinbaidar: if you can confirm that whereami still crashes the AFNI GUI when you have an active internet connection, would you mind emailing me your dwm and any relevant configs? I can try and test your setup later this week.

ptaylor.afni commented on 2022-10-31 14:11 (UTC)

@nikinbaidar: By default, the whereami functionality in the GUI tries to connect to the NeuroSynth webpage. If it can't do so (e.g., you are offline), then it can crash on some systems. You should check if you are online or not.

You can tell the afni GUI not to try to connect to NeuroSynth by setting this environment variable in your ~/.afnirc settings file: AFNI_WEBBY_WAMI = NO

Also, as Daniel noted here: https://afni.nimh.nih.gov/afni/community/board/read.php?1,163424,163426#msg-163426 ... you should check that your machine has an X11 server that supports X11 HTML (like VcXsrv).

--pt

nikinbaidar commented on 2022-10-30 07:08 (UTC)

I don't know what exactly is causing it but in AFNI when I have an image open and I do right click and select whereami, the whole program crashes. I don't know if this happens in only my system, I am on xorg and dwm.

keiichiiownsu12 commented on 2022-10-04 22:14 (UTC)

Just a heads-up: systems that have llvm installed will cause conflicts with afni scripts that depend on /opt/afni/count. E.g. @chauffeur_afni is unable to determine the X-display due to dependency on /opt/afni/count for rng. I am not sure of a decent way to fix this, other than defining a new alias in shell-rc files that points to /opt/afni/count...

liamtimms commented on 2022-09-30 15:22 (UTC)

@keiichiiownsu12 sounds good, let me know if you need help along the way. Once a package is put together, it's much easier to keep maintaining it in most cases.

keiichiiownsu12 commented on 2022-09-30 15:13 (UTC)

Also, @liamtimms: I'll get an afni-atlases package going over the next week. Since that would be my first package I'd be maintaining, I'll ask you to review the PKGBUILD and any patches for this repo before submission by next week, if that is okay with you.

keiichiiownsu12 commented on 2022-09-29 21:42 (UTC)

@liamtimms: sure thing. I'd be happy to co-maintain. Please be aware, this would be my first package I'd be maintaining on the AUR.

liamtimms commented on 2022-09-29 19:47 (UTC)

Thanks, @keiichiiownsu, and @ptaylor.afni; I have added the dependency and updated it to the latest tagged version. I will also mention again that I would be open to adding a co-maintainer to keep this a bit more rapidly updated.

ptaylor.afni commented on 2022-09-28 21:43 (UTC)

@keiichiiownsu12 : Well, actually the xvfb dependency unlocks a widely used functionality to output QC images for major processing steps, esp. for afni_proc.py (FMRI pipeline creation), @SSwarper and @animal_warper (skullstripping and nonlinear template alignment/warping), @afni_refacer_run (refacing/defacing datasets, to anonymize them), the FATCAT processing programs for DWI processing, and more. I would strongly recommend any AFNI user to have that functionality available.