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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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Hello,
I am hoping to gray matter mask my fMRI data at the individual subject level to be more consistent with analyses collaborators are using in other imaging softwares. Presently, we use afni_proc.py to preprocess data without any masking, 3dDeconvolve for individual subject GLMs, and 3dLME for group level analyses, in which we apply a whole brain mask. It's not immediately clear to me
by
alibc90
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AFNI Message Board
Hello!
I was wondering if instead of the options listed for extracting the ROI time series and detrending (from ), it would be alright/equivalent to run 3dDeconvolve to remove the trend and account for motion, collect the residuals, then use the residuals for ROI time series extraction and proceed as outlined? Sample script below
Thank you for your time!
Ali
3dDeconvolve \
by
alibc90
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AFNI Message Board
it seems that configuring our R3.1.1 install with the --enable-R-shlib flag did the trick. Thanks so much for your help!
by
alibc90
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AFNI Message Board
thanks, rick. the file does seem to exist
the output is:
-rwxr-xr-x 1 caseylab_curate caseylab 4414026 Sep 16 10:27 R_io.so
by
alibc90
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AFNI Message Board
R3.1.1 installs fine and `make check` verifies the installation of basic packages.
however, we still get the R_io.so message when we run 3dLME
output of R --version
"R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
"
by
alibc90
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AFNI Message Board
Hi Gang,
We have tried R-2.15.1 R-2.15.2 and are currently unsuccessful with R-3.1.1
by
alibc90
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AFNI Message Board
We have come across the R_io.so problem in trying to run R commands on a shared server. Unforunately, all the specified troubleshooting on has not worked so far. Requested information copied below:
1. Error in dyn.load(ll) :
unable to load shared object '/zenodotus/caseylab/store/users/caseylab_curate/software/abin/R_io.so':
libR.so: cannot open shared object file: No suc
by
alibc90
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AFNI Message Board
Hi Gang,
1) The error RE parameters is:
** Error:
Expecting 1 to 10000 parameters for option "-dataTable".
Have 10717 parameter(s) in string
However the number of lines after dataTable is 2647 (147 subs * 18 subbriks + 1 line specifying inputs)
2) The error for a subject with missing subbriks is
Error in dim(inData) <- c(dimx, dimy, dimz, NoFile) :
dims do no
by
alibc90
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AFNI Message Board
Hi,
I'm trying to run a 3dLME with 147 participants (and counting!) and a fairly large model (Context*Cue*Target*AgeGroup+Peer) but am running into several errors.
1) 3dLME returns the message that it is limited to 10,000 parameters and since each participant has 18 regressors (!) this is not enough for the full model
2) A few subjects are missing certain regressors and 3dLME seem
by
alibc90
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AFNI Message Board
Great, thank you!!-- I did think this was odd, but 3dFoodie is my labmate with the same computer and this supposedly worked for him but perhaps there was a miscommunication :)
by
alibc90
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AFNI Message Board
Hi Rick,
I ran software updates and rebooted several times still get the same error (below) when typing "afni -ver" into the command line of my terminal. The OS version of my machine is 10.6.8
dyld: Library not loaded: /usr/X11/lib/libX11.6.dylib
Referenced from: /Users/alicohen/abin/afni
Reason: Incompatible library version: afni requires version 10.0.0 or later, but libX
by
alibc90
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AFNI Message Board
Hello,
I'm getting the "Failed to load R_io.so" error in addition to several others but first thing-- I tried updating my binaries as suggested, received the message "no update needed" and then when typing afni -ver get the message
dyld: Library not loaded: /usr/X11/lib/libX11.6.dylib
Referenced from: /Users/alicohen/abin/afni
Reason: Incompatible library ver
by
alibc90
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AFNI Message Board
Apologies for the delayed response-- there do not seem to be major differences besides naming conventions, but I'm just (perhaps irrationally?) worried about continuing to operate from these older binaries. But this seems like a fine work around. Just wondering if there had been any updates!
Thanks!
by
alibc90
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AFNI Message Board
Hello,
I encountered a similar problem with freezing while trying to run 3dQWarp (on Mac OS X version 10.6.8) and downloaded the Intel compiler to overcome the complete freeze. Shutting off OpenMP was too slow/not deemed to be a good idea by the more tech saavy people in the lab. It runs alright, but I've noticed that the outputs from afni_proc.py are somewhat different using these bin
by
alibc90
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AFNI Message Board