Package Details: afni 24.3.03-1

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, ajschadler12)
Last Packager: ajschadler12
Votes: 1
Popularity: 0.000000
First Submitted: 2016-06-29 01:28 (UTC)
Last Updated: 2024-10-21 17:18 (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 Please do not flag this package "out-of-date" without some technical justification.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 2022-01-21 14:27 (UTC) (edited on 2022-01-21 14:28 (UTC) by ptaylor.afni)

Re. the atlases distributed in AFNI (relevant for @liamtimms):

  • we have simplified the packaging of these, so that the single tarball "atlases_current.tgz" from https://afni.nimh.nih.gov/pub/dist/atlases/ should be all that is needed. Note that untarring that file should not splash files around the PWD, either, anymore... yikes.

Re. this comment "REALLY wish they'd make this easier to find...: link to other atlas files..." (relevant for @keiichiiownsu1 and @kcdah):

  • We have added a new webpage to the main documentation (https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/template_atlas/other_tas.html), listing+linking all the templates and atlases (it is under the "Templates & Atlases" section, as well as under the "Non-human processing" one, because both human and non-human datasets are contained there). We do welcome helpful suggestions---again, we have a higher chance of seeing them on the project github page.

ptaylor.afni commented on 2022-01-21 14:19 (UTC) (edited on 2022-01-21 14:19 (UTC) by ptaylor.afni)

Hi- We are happy to see this project of building+distributing AFNI on ArchLinux systems. Please ping us with any questions, as they arise. It might be easiest to do so via an Issue on the project's main github page: https://github.com/afni/afni

A couple of notes about issues raised here already, since the discussions did make it to the github page (and sorry, I don't see how to reply to a thread directly):

nikinbaidar commented on 2022-01-11 02:07 (UTC) (edited on 2022-01-14 12:23 (UTC) by nikinbaidar)

Hello, I am very new to AFNI. I installed it with yay and updated my path var as PATH=${PATH}:/opt/afni. AFNI runs and all but I cannot find the 3DSkullStrip program. The output of ls /opt/afni | grep -i skull is @NoisySkullStrip @SkullStrip_TouchUp

Where can I find the 3DSkullStrip? Or is it even installed?

Edit:Okay turns out suma needs to be installed to run that program. But I am not sure how to do that either.

liamtimms commented on 2021-12-20 17:06 (UTC)

Running into this error on the latest version of AFNI and have not had time to investigate further so I'm not updating the PKGBUILD to the most recent release for a while:

/usr/bin/ld: ./libcoxplot.a(pwritf.o):(.bss+0x80): multiple definition of `zzzplt_'; ./libcoxplot.a(ppak_commons.o):(.bss+0xc0): first defined here
/usr/bin/ld: ./libcoxplot.a(pwritf.o):(.bss+0x0): multiple definition of `zzpltr_'; ./libcoxplot.a(ppak_commons.o):(.bss+0x40): first defined here
/usr/bin/ld: libXmHTML.a(LZWStream.o): in function `LZWStreamInit':
LZWStream.c:(.text+0xdd3): warning: the use of `tmpnam' is dangerous, better use `mkstemp'

liamtimms commented on 2021-07-02 16:50 (UTC)

@keiichiiownsu12 thanks I generally only use the CLI and haven't done any GUI testing. If you figure out what is causing those segfaults and how to fix them I'd gladly add you as a co-maintainer. For question about python2 and python3 there's a concept in Arch to handle that called "split packages" which can provide both versions, however I haven't tested or looked at whether that actually makes sense here.

keiichiiownsu12 commented on 2021-07-01 00:04 (UTC)

@liamtimms some afni python programs are able to open a GUI (e.g. uber_ttest.py), but they require python-pyqt4 as a dependency. Maybe you can include it as an optional dependency? (or a similar package). Though some GUI python commands (e.g. uber_subject.py) segfault when run... Maybe there is a package that can work for BOTH python3 and python2?

More of an advisory: most python programs appear to be written in python2 (for whatever reason). Python3 compatibility seems to be...variable for most. If you run into problems, just execute them with a python2 interpreter python2 `which <cmd>.py`

kcdah commented on 2021-05-06 23:01 (UTC)

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

keiichiiownsu12 commented on 2021-05-05 22:00 (UTC)

@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.

keiichiiownsu12 commented on 2021-05-05 21:47 (UTC)

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

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