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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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Results 31 - 60 of 143
Hi,
From Paul:
https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Linux
In the end this procedure worked to get brms:
# Add Michael Rutter's c2d4u3.5 PPA (and rrutter3.5 for CRAN builds too)
sudo add-apt-repository -y "ppa:marutter/rrutter3.5"
sudo add-apt-repository -y "ppa:marutter/c2d4u3.5"
sudo apt update
sudo apt install r-cran-rstan
sudo
by
discoraj
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AFNI Message Board
Hi,
If you don't like zsh you can change it with instructions here:
https://support.apple.com/en-us/HT208050
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Let's see if macOS has given you some extended attributes.
Can you run in the terminal?:
xattr ~/abin/afni
Can you post what you get (if you get something)?
If you do get something, you can remove the extended attributes with:
xattr -cr ~/abin
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
A few questions:
What procedure did you use to install afni?
Did you upgrade from 10.14 to 10.15 or is it a clean install?
What shell are you using? get the output from:
echo $0
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
I am not sure about the python error, but the ones from the command line are just warnings. And you should be fine as long as the rest of the afni_sysyem_check was ok.
I think the python error may be from the app trying to use the default python to run afni_sysyem_check.py
I can look into that.
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
We could try a remote support screen share.
Email me at:
rajendrajk@nih.gov
So we can set up a time.
by
discoraj
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AFNI Message Board
Hi,
----------------------
Possible certificate problem:
Open "Keychain Access" in Applications -> Utilities
Search for "DigiCert"
From the "View" menu select "Show Expired Certificates" (All of my DigiCert certificates expire sometime in the 2030's)
If there is an expired one, delete it (right click and choose delete), restart and try th
by
discoraj
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AFNI Message Board
Hi,
Both the Zscr and the one sample ttest problems are on my end...
It never occurred to me to look at a one sample test with box plots, but it makes total sense.
I may have left it out because I haven't yet added support for covariate files.
The error caused by the program looking for 2 labels for the 2 groups in the case of 3dttest++
I can try to get fixes in over the weekend.
by
discoraj
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AFNI Message Board
Hi,
I am going to split this thread into a new one for a cleaner topic.
Follow up here:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,162101,162101#msg-162101
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Just redirecting a thread to a new one.
Original question was:
Dear Justin,
this morning we run Cluster Explorer with the results derived from one sample t-test executed with 3dttest++. It didn't work, likely because the output was Zscr. We have tried to run it with an output based on t stat, but we obtained the following error message when executing @ClustExp_run_shiny:
At
by
discoraj
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AFNI Message Board
Hi,
hmm, a couple of ideas.
1.
What happens when you go to https://github.com/Homebrew/homebrew-core in a browser?
If there is a problem, it could be your organization's firewall or a DNS problem. (I doubt it...)
If it is the case that it is a problem connecting and if the machine is a laptop, try installing from another network.
If you can connect to github, what happens when you
by
discoraj
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AFNI Message Board
hi,
It could be a few things.
First try:
brew doctor
brew cleanup
brew update
Then restart the computer and try the installer again.
If that doesn't help, can you look at your .bash_profile or .bashrc and see if there is anything strange in there.
Like a change in your path that you don't expect or a configuration program running.
If you have anaconda or conda in your path,
by
discoraj
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AFNI Message Board
Hi,
What is the max displacement for your data? There should be more info in the summary saved after the afni_proc script is executed.
How many time points?
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Is it possible that the censoring is coming from the outliers and not the motion?
thanks, Justin
by
discoraj
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AFNI Message Board
I think I need to punt this one to Bob...
One question is, from where are you calculating the channel-channel covariance?
by
discoraj
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AFNI Message Board
Hi,
Bug squashed.
It was a header reading error when an ROI label starts with the same characters as a statistic code.
Update coming in next build.
Thanks for bug hunting, Justin
by
discoraj
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AFNI Message Board
Hi,
What proper cluster statistical analysis did the reviewer suggest?
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
I am going to add the ability to check for and use zscores.
Hopefully soon.
For the 3dMEMA, I need to consult with Gang a bit so that may take more time.
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Can you send me your .netcc file (rajendrajk@nih.gov)?
or post it here if it is not too huge?
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
The ClusterExplorer needs the Tstat AND the degrees of freedom from the image header.
Can you run 3dttest++ without the corrections just to look at the clusters?
The coordinates of the peak voxels of the clusters could be pretty close but the center of mass of the clusters could be very different and the clusters themselves could be different.
I should be able to add a check for the z-sc
by
discoraj
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AFNI Message Board
Hi,
Try changing "-ThreshBrik 0" to "-ThreshBrik 1"
The program is looking for some statistic in the header.
I have not tested this with Zscr stats...
I am pretty sure it won't work with Zscr as there is no degrees of freedom associated with it.
I can work on adding support for the z score and cleaning up the error message.
In the meantime, you could try runnin
by
discoraj
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AFNI Message Board
Hi,
Could you tell us about the data that was collected?
Was there any physiological data collected with the scans?
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
You should try the ClusterExplorer to make it a little easier.
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/ClusterExplorer/Introduction.html
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Can you try installing gdal separately? (Geospatial Data Abstraction Library)
yum install gdal-devel
That is needed for iGraphs, but iGraphs is not really necessary for what we do with brms.
Unfortunately, the brms library has a lot of extra stuff for visualization that bloats the install and has nothing to do with just doing the analysis.
Could be handy, but not really for us at t
by
discoraj
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AFNI Message Board
Hi,
I am a little late, but you could try the 3dMVM_validator to test your model and GLTs and it will create the 3dMVM script for you.
So you don't have to worry about the extra spaces.
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/3dMVM_validator/3dMVM_validator_overview.html
thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
If you are up to date on afni, you should be able to run the FATCAT_matplot without the -ShinyFolder option.
I can upload the current shiny folder, but you already have it and FATCAT_matplot will find it by default.
FATCAT_matplot /data/data05/naveed/1.Projects/7.MCSA_rs-fMRI/BS0001MC_20180315.results
And the tutorial is here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutoria
by
discoraj
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AFNI Message Board
Hi,
This folder seems to be wrong:
/home/naveed/R/x86_64-pc-linux-gnu-library/3.4/shiny/FATCAT_matplot_shiny
That does not seem to be one of our folders. It looks like an R library folder.
Were you able to download the new FATCAT_matplot?
It should find the correct folder for you now.
If that doesn't work, I can send you the most up to date FATCAT_matplot_shiny folder.
thanks, Just
by
discoraj
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AFNI Message Board
hi,
try this:
@FATCAT_matplot_shiny -ShinyFolder /home/naveed/R/x86_64-pc-linux-gnu-library/3.4/shiny/FATCAT_matplot_shiny BS0001MC_20180315.results
It is designed to read all of the matrix like files in that folder.
Also the -ShinyFolder needs the folder with the shiny app in it.
The -ShinyFolder is mainly for testing different versions of the app.
Here is a link to the latest FATC
by
discoraj
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AFNI Message Board
Hi,
Can you try it with 3dcopy?
3dcopy my_data+orig my_data.nii.gz
Thanks, Justin
by
discoraj
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AFNI Message Board
Hi,
Getting close.
That looks like an old version of afni, but that should be fine.
(I dropped the @ in later versions because of osx tab completion failures....)
The program will look for a folder containing the .netcc files.
Try just having the last argument point to the folder instead of the files.
There was a bug some time ago that caused the program to choke if there were non matrix
by
discoraj
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AFNI Message Board
Page 2 of 5
Pages: 12345