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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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I would argue that it's acceptable to let somebody copy it out of the BIDS tree. Another alternative would be a -debids_to option where as much information as possible from the sidecar is put into the AFNI extension and a new dataset that is NOT intended to be BIDS-compliant output.
by
jbteves
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AFNI Message Board
Yeah, some joker on the internet gave it to me! You can trust these things without looking at them at all.
It's not too complex to add one, I could do that today if I can remember how to set up the dev environment correctly for the python scripts.
by
jbteves
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AFNI Message Board
Sure,
3drefit -Tslices 0.0 0.05319 0.10638 0.15957 0.21277 0.26596 0.31915 0.37234 0.42553 0.47872 0.53191 0.58511 0.6383 0.69149 0.74468 0.79787 0.85106 0.90426 0.95745 1.01064 1.06383 1.11702 1.17021 1.2234 1.2766 1.32979 1.38298 1.43617 1.48936 1.54255 1.59574 1.64894 1.70213 1.75532 1.80851 1.8617 1.91489 1.96809 2.02128 2.07447 2.12766 2.18085 2.23404 2.28723 2.34043 2.39362 2.44681 /gpfs/g
by
jbteves
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AFNI Message Board
The thing is that the error happens intermittently, I didn't think to save a copy of the dset that was corrupted, but simply replacing it with the original file did the trick, and re-running caused the error to go away. I agree that it would be could for abids_tool.py to terminate, but poking around it looks like the issue is that 3drefit is not actually giving a non-zero exit, so abids_tool
by
jbteves
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AFNI Message Board
Addendum: what is happening is not quite what I reported. What seems to be happening is that because I'm using abids_tool, if there is a read error from the filesystem it consequently writes out a corrupted file in the same spot (the error does not cause the program to terminate, so it continues on by writing the existing, corrupted, data back to disk in the same filename). Using pigz does s
by
jbteves
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AFNI Message Board
I actually just opened up a similar topic, and intriguingly this does appear to be OS or machine-dependent behavior: I'm seeing the error on biowulf but not on MacOS.
by
jbteves
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AFNI Message Board
When running abids_tool.py, an error is triggered on biowulf but not locally:
++ WARNING: nifti_read_buffer(/gpfs/gsfs12/users/tevesjb/Frontiers_QC_2022/osfstorage-archive/fmri-open-qc-task/sub-001/func/sub-001_task-pamenc_bold.nii.gz):
data bytes needed = 278528
data bytes input = 216336
number missing = 62192 (set to 0)
** NIFTI load bricks: cannot read brick 19 from '/gp
by
jbteves
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AFNI Message Board
I do typically place a #! directive at the top, though in these newer days of zsh it looks a bit different from bash-is-default days of yesteryear on MacOS.
I have never experimented with tcsh though.
by
jbteves
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AFNI Message Board
I'm using zsh, and indeed sourcing the zshrc in the script seems to work.
This is a very annoying MacOS quirk, though somehow I haven't run into it before... And a very interesting failure mode.
Fortunately I already had the DYLD path in my zshrc, so with it sourced things proceed fine.
Thanks for the rapid feedback!
by
jbteves
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AFNI Message Board
AFNI fails with the following error message:
Fatal Signal 11 (SIGSEGV) received
open_MCW_imseq
SPLASH_popup_image
AFNI_splashup
MAIN_workprocess
AFNI:main
Bottom of Debug Stack
** AFNI version = AFNI_22.1.14 Compile date = Jun 24 2022
** []
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and
by
jbteves
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AFNI Message Board
Hi Doug,
Which tedana version would you like to use? If you want to use the tedana packaged in abin/, you'll probably need to use a python 2 environment as it's python 2. In order to use a more modern tedana (which would be my current recommendation), you'll want to, in your current environment, run:
pip install tedana
to get the latest version. Then, in your afni_proc scrip
by
jbteves
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AFNI Message Board
You might check out this article on slice timing and modeling if you are concerned:
by
jbteves
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AFNI Message Board
Iliara,
I would not consider myself an AFNI expert, but I would not recommend "mixing and matching" these preprocessing pipelines, as neither of them are designed to interoperate. fMRIPrep is intended to replace all other programs' preprocessing, by doing the "mixing and matching" between major packages for you. If your plan is to do a GLM, etc. in AFNI then I would reco
by
jbteves
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AFNI Message Board
Okay, you can't use brew in this configuration because the other user is the owner of it. You will need to install brew into your home directory or some other location that you have permission to access in order to probably use it. Brew should support this by asking for the location you would like to install into when you begin the installation process (choose maybe ~/homebrew).
by
jbteves
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AFNI Message Board
Is IRM2 your username? Those permissions look correct. If you're not sure, you can run
echo $USER
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jbteves
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AFNI Message Board
This is a brew rather than AFNI problem, but it looks like your brew installation set the owner of all of your homebrew configurations to root, rather than to your user. If you run
ls -l /usr/local/Cellar/pkg-config/
I suspect it will show the owner as "root," rather than your username, OR that your permissions lack read permission for you. What's the output of that ls comman
by
jbteves
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AFNI Message Board
dcm2niix is maintained by Chris Rorden. You could open an issue here: though I suspect he will be of the opinion that it's better to spew too many messages than too few. It is packaged with AFNI for everyone's convenience as it is a very popular and useful tool.
Practically speaking, the solution is probably just for you to use `grep` to filter out those warnings. You could try this
by
jbteves
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AFNI Message Board
Hello,
This is the AFNI forum, and the function that produced it is an FSL function. So you may want to ask that question over at their mailing list:
That said, what are you trying to open this file with? If it is an AFNI program, then it is not designed to load an FSL file. If you are using Matlab to open it (which is what your OS will default to if you click on it) then it will attempt to re
by
jbteves
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AFNI Message Board
Hm, I don't remember doing this but I also did it approximately 3/4 of a pandemic ago. Is there any compelling reason not to just build from the tip of the latest master if I feel adventurous?
by
jbteves
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AFNI Message Board
I meant to type 10.15, whoops.
What's the best way to update the binaries for AFNI in this configuration?
by
jbteves
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AFNI Message Board
I'm very confident that I'm simply doing something wrong, but if I run
@update.afni.binaries -defaults -do_extras
Then I get the following error:
-- running @update.afni.binaries version 3.16, September 16, 2020
-- have AFNI binaries under /Users/tevesjb/abin
-- install dir: using existing /Users/tevesjb/abin
-- any downloads will be from via curl -O -f
-- attempting to inst
by
jbteves
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AFNI Message Board
Further update: after building AFNI from the MacOS 10.15 makefile, I still see a shared memory error, but no longer receive SIGSEV and AFNI appears to be receiving real-time data. Perhaps an issue with the way things are configured in the default MacOS binaries?
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jbteves
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AFNI Message Board
Rick, on a different Ubuntu machine it does not show flat_namespace (In fact, DYLD_LIBRARY_PATH is entirely blank). What should I make sure gets linked?
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jbteves
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AFNI Message Board
> If you run the script but not rtfeedme, are there any issues looking at datasets in that directory?
I'm not sure what the script is in this context, but there are no issues loading the files in the AFNI viewer in the directory where I'm calling rtfeedme
> Do the __001 (etc.) datasets exist? Can you view them with the GUI?
They are not generated when I run rtfeedme, no.
by
jbteves
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AFNI Message Board
Hi Rick,
This is the result after real-time AFNI begins listening:
RT: starting to listen for control stream.
PO: plugout connection from host 127.0.0.1 (tcp:*:7955)
PO: plugout connection name is plugout_drive
DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
PO: plugout 'plugout_drive' has broken connection!
: iochan_goodcheck: no longer alive
by
jbteves
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AFNI Message Board
Unfortunately the issue remains, but at least now we're rid of the shared memory issue:
RT: connected to control stream 127.0.0.1
RT: version 23 Jan 2020: ROIs_and_data
RT: init RT input via control channel
RT: waiting for data stream to become good.
RT: receiving image metadata=164 bytes
RT TIME (starting to receive realtime data): 2128 sec, 434 ms (0 ms passed)
## PARSE RT Detrend
by
jbteves
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AFNI Message Board
Versions of relevant programs:
- MacOS 10.15.7 "Catalina" (I know, I know...)
- AFNI 2021-03-24
- Xquartz 2.8.0
In one terminal, with the following environment variable modifications:
export AFNI_REALTIME_Registration=3D:_realtime
export AFNI_REALTIME_Base_Image=2
export AFNI_REALTIME_Graph=Realtime
export AFNI_REALTIME_MP_HOST_PORT=localhost:53214
export AFNI_REALTIME_SEND_V
by
jbteves
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AFNI Message Board