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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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Hi,
I tried it with 2002 input files and it runs fine.
I think it it may be your really long file paths.
There is some limit in the shell to the number of characters that can be used as an argument.
Not sure what that is, but you may be running into that limit.
I think moving your data to a folder with a shorter path may be painful.
So maybe try modifying your csv file to remove this p
by
discoraj
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AFNI Message Board
Hmm.
I never tried this with so many datasets at once.
I didn't expect there to be a limit on input datasets for 3dcalc.
I'll do some checking and testing.
Thanks, Justin
by
discoraj
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AFNI Message Board
No problem.
This is what we are here for.
Let me know if you have any more questions.
thanks, Justin
by
discoraj
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AFNI Message Board
hmm.
quit and restart your terminal. (restarting the whole machine would be better)
Then try again.
If you get the same thing, try this:
echo 'export PATH=$PATH:/Users/mollywilkinson/abin' >> ~/.zshrc
source ~/.zshrc
This assumes you used the defaults for the afni installation.
by
discoraj
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AFNI Message Board
Do the same chown for the other .files.
sudo chown mollywilkinson ~/.bashrc
sudo chown mollywilkinson ~/.cshrc
sudo chown mollywilkinson ~/.tcshrc
Just run the tcsh @update.afni.binaries -package macos_10.12_local -do_extras again.
If there are any other files giving you permissions problems, check the owner with the ls -al.
Then fix the ownership as above.
You may want to try and figu
by
discoraj
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AFNI Message Board
sorry, artifact of the message board messes up the web addresses if I don't pay attention...
try this
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
by
discoraj
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AFNI Message Board
You should be able to delete the last 3 lines as they are repeats.
I don't see any illegal names.
Quit the terminal if you aren't using it and restart your machine.
Then just continue with the next steps (Rscript, curl etc)
by
discoraj
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AFNI Message Board
Hi,
Ok. seems like .zshrc was created by root or using "sudo".
you can reclaim ownership with:
sudo chown mollywilkinson ~/.zshrc
Then continue to run the original instructions.
HOWEVER...
The M1 version may have some different path settings, so we will have to deal with that when you get to it.
Unfortunately I don't have my M1 at the moment, but I think we can figure
by
discoraj
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AFNI Message Board
hmmm.
Strange you don't have permissions for that file (.zshrc).
can you run?:
ls -l ~/.zshrc
The output should look something like this:
-rw-r--r-- 1 discoraj staff 993 May 13 12:41 /Users/discoraj/.zshrc
Your username should be the owner (where it says discoraj for mine).
Did someone else create that file?
Can you run:?
cat ~/.zshrc
And post the output.
Let's
by
discoraj
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AFNI Message Board
Hi,
Glad it works.
There will be some packages missing from afni_system_check.
This should get most of them, but not all:
Rscript -e "install.packages(c('phia','snow','nlme','lmerTest'),repos='https://cloud.r-project.org')"
Some of the packages are not available on mac with R 3.6.3.
We are working on compiling for R 4.
Thank
by
discoraj
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AFNI Message Board
Hi,
Do you have admin access on your computer?
You can check with:
sudo ls
I am working on some better instructions for macOS 12.3.1 and greater including M1.
But there are no pre-compiled afni binaries for the M1 (or upcoming M2) as of yet.
Soon! Pre-compiled apple silicon (M1 etc) will be faster, but with rosetta 2, it is not that much slower.
If you do have admin access and macO
by
discoraj
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AFNI Message Board
Hi,
Here are a few things you can try:
For gfortran you can install a version that R 3.6 uses.
Run this at the terminal:
curl -s -L -o gfortran-6.1.pkg "https://cloud.r-project.org/bin/macosx/tools/gfortran-6.1.pkg"
sudo installer -pkg gfortran-6.1.pkg -target /
rm gfortran-6.1.pkg
You need this to your path before you try to use it
/usr/local/gfortran/bin
For 3dMV
by
discoraj
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AFNI Message Board
Hi,
Some functions were changed or deprecated with updated libraries.
I'll update the binaries with the fixes.
But you can use this in the meantime:
MyOutput_ClustExp_shiny_edit.zip
and this message is normal and not an error:
PO: plugout 'plugout_drive' has broken connection!
: iochan_goodcheck: no longer alive
You can use the .csv files in the "data"
by
discoraj
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AFNI Message Board
Hi,
Try:
brew install openmpi
If that fails, there is a gfortran installer from R (cran)
See this:
Separate issues but one may help
by
discoraj
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AFNI Message Board
Hi,
Any chance you can try with firefox?
The slider error is from the R code running in the browser.
Not with the afni gui.
I'll double check the code to see if there is a error check I can put in.
If firefox doesn't work , can you post your commands?
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Can you post the output of:?
afni_system_check.py -check_all
Thanks
by
discoraj
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AFNI Message Board
Hi,
What version of R do you have installed?
If it is greater 4 or greater, you can run this from R:
(you should be able to start R at the terminal by typing):
R
Then run this in R
install.packages("BiocManager",repos=";)
BiocManager::install("OmicCircos")
then to quit R:
q()
I'll put in a check for this in the next release.
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Can you send me your input table to:
justin.rajendra @ nih.gov
(Without the spaces)
And the output of:
afni_system_check.py -check_all
Would be helpful as well.
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Can you post your commands and the output of:
afni_system_check.py -check_all
?
Also, if possible can you email your csv file to justin.rajendra@nih.gov?
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Does afni without the -niml work?
And suma separately?
thanks, Justin
by
discoraj
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AFNI Message Board
hmm...
I ran into the data.table problem on 10.15 as well.
I solved it by installing it manually from within the R GUI (not R studio or command line)
I think that the R libraries must be getting installed in separate places for all of the different versions of R.
Try installing all of the necessary libraries in all of your R instances.
You can find the library location with
.Library
by
discoraj
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AFNI Message Board
hi,
Is your macOS firewall enabled?
( System Preference -> Security & Privacy -> Firewall )
When you first opened xquartz or ran afni, was there a mac popup that asked to "accept incoming connections"?
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Try adding this to your .zshrc (create it if it is not there)
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace
and to remove the errors you see, you can comment out from your zshenv or where ever it is:
if [ -f $HOME/.afni/help/all_progs.COMP.bash ]
then
. $HOME/.afni/help/all_progs.COMP.bash ]
fi
That may get rid of the errors, but you won'
by
discoraj
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AFNI Message Board
Hi,
For "Operation not permitted" errors:
Try going to the System Preferences, then Security & Privacy, then Full Disk Access.
Then make sure that launchd_startx, Terminal, and XQuartz are there and checked.
See attached.
You will need admin access.
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Try this for ideas.
It will plot interactions to see direction etc.
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/ClusterExplorer/Introduction.html
thanks, Justin
by
discoraj
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AFNI Message Board
Give this a try:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/3dMVM_validator/3dMVM_validator_overview.html
by
discoraj
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AFNI Message Board
Seems like my PMs are not sending...
email is discoraj@gmail.com
by
discoraj
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AFNI Message Board
Hi,
Can you post the code that you used for the analysis?
And send me your outputs?
Thanks, Justin
by
discoraj
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AFNI Message Board
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Pages: 12345