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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely,
AFNI HQ
History of AFNI updates
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Pages: 123
Results 61 - 80 of 80
afni -ver
Precompiled binary linux_ubuntu_16_64: Mar 3 2021 (Version AFNI_21.0.13 'Titus')
@animal_warper -ver
3.31
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[1]. (I am modifying MACAQUE_DEMO_REST for my purpo
by
Pawel
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AFNI Message Board
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
("-outdir ..")
[..]
+ Template dsets and followers in template space
by
Pawel
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AFNI Message Board
Thank you, this generated correct proc script. Now running it, fingers crossed!
by
Pawel
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AFNI Message Board
Hello,
I am modifying MACAQUE_DEMO_REST to work with my data. Experimenting with EPI-anat alignment, I found that EPI stripping with 3dAutomask fails with my data but stripping with 3dSkullStrip works fine.
So in my modified script I start afni_proc.py with the following options:
set cost_a2e = "lpa+ZZ"
[...]
afni_proc.py
by
Pawel
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AFNI Message Board
Thank you. I am sticking to WSL 1 for two reasons: first, as you said, CIT keeps us on a version of Windows that does not run WSL 2. Second, it seems that getting AFNI GUI to work on WSL 2 is over complicated... I tried it on a non-gov machine with WSL 2, ran into problems, got some suggestions from you (https://afni.nimh.nih.gov/afni/community/board/read.php?1,159772,165003#msg-165003) but they
by
Pawel
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AFNI Message Board
Whatever the name will be, is there a plan when the name would be available?
by
Pawel
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AFNI Message Board
"being integrated a bit with another project (SARM)"
Does this mean that they will be combined into FARM (Full hierarchical Atlas of the Rhesus Monkey brain) at some point? That could be useful!
by
Pawel
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AFNI Message Board
Hello,
this is not really an AFNI question but it is related to using AFNI so I hope it's still OK to post.
I am encountering a weird problem while using AFNI on an NIH-owned Windows laptop, working from home.
AFNI is installed on Ubuntu 18.04 which runs on WSL 1.
As an NIH employee, every now and then I have to VPN to NIH network to do various things that are not accessible fro
by
Pawel
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AFNI Message Board
Hi everyone,
I recently went 3 times through installing AFNI on Ubuntu 18.04 on WSL1 on Windows 10, and each time I run into a problem with installing brms, which was not solved by the suggested solution, i.e.:
sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"
sudo apt update
sudo apt install -y r-cran-rstan r-
by
Pawel
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AFNI Message Board
Thank you, Daniel. Much of your response is completely cryptic to a Windows simpleton like me
I tried the initial part, (export DISPLAY="$(/sbin/ip route | awk '/default/ { print $3 }'):0") plus changing VcxSrv options, but that got me nowhere.
So I switched to WSL 1 and both AFNI and SUMA GUIs start fine. Thanks a lot!
by
Pawel
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AFNI Message Board
I am reviving this thread because I ran into the same problem though in a new installation and under different circumstances.
So I just installed AFNI on a windows computer, using instructions from
and
The installation went kind of OK, bdrm would not install despite trying the suggested fix (If you are using Windows Subsystem Linux (WSL), and/or if your ‘brms’ package fails to install
by
Pawel
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AFNI Message Board
ptaylor Wrote:
-------------------------------------------------------
> Re. the $DISPLAY variable,
> what does:
> echo $DISPLAY
> do?
:0.0
This is still remotely, again, I can recheck locally on Monday
by
Pawel
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AFNI Message Board
ptaylor Wrote:
-------------------------------------------------------
> What version of linux do you have? That is, what
> is the output of:
> lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 16.04.4 LTS
Release: 16.04
Codename: xenial
>
> Note that you can preserve your tailorings
> (though, I'
by
Pawel
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AFNI Message Board
I am getting this message when trying to start AFNI:
Initializing: X11Error: Can't open display:
++ AFNI is detached from terminal.
Any ideas how to fix it?
Story behind:
AFNI Installed on Win10/WSL/Ubuntu a few months ago, without major problems (there was a dependency problem with encryption libraries, but good linux-knowing people helped me solve it)
I've been using AFNI
by
Pawel
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AFNI Message Board
This^^^
I got the same advice from elsewhere, and
sudo apt-get install libssl-dev
followed by another
rPkgsInstall -pkgs ALL
solved the brms installation problem
(or at least AFNI check did not complain about anything anymore)
by
Pawel
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AFNI Message Board
Thank you. This did not help though, I got:
E: Unable to locate package openssl-dev
But someone else recommended
sudo apt-get install libssl-dev
and after that, and reinstallation of R, AFNI installation check return a yay!
by
Pawel
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AFNI Message Board
I tried installing libcurl4-openssl-dev as suggested by isospin in the "brms not installed" thread.
This fixed the afex and phia problem, but brms is still reported not installed.
It looks to me that PKI fails to install due to lack of openssl (even though I did sudo apt-get install libcurl4-openssl-dev) and that leads to brms not installed through a chain of dependencies
Any
by
Pawel
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AFNI Message Board
Hello helpful people,
I am trying to install AFNI for the first time in my life. On Windows/WSL/Ubuntu
I followed instructions at faithfully (I think), but
afni_system_check.py -check_all
returns
Quote========================= summary, please fix: =========================
* missing R packages (see rPkgsInstall)
and
Quotechecking for R packages...
rPkgsInstall -pkgs AL
by
Pawel
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AFNI Message Board
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Pages: 123