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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 Gang et al.,
I've been using 3dLMER to identify clusters of interest but want to know how I might be able to also extract beta parameters for the contrast(s) of interest for each subject for subsequent analyses from the output. Is there another program I could use in tandem that would accomplish what I'm trying to achieve?
Thank you in advance!
Amar
by
aojha17
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AFNI Message Board
Hello Gang et al.,
I have a 3dLMEr modeling question I am hoping you may be able to help with.
Is it possible to specify multiple contrasts in one model? Essentially, we have a Negative, Neutral, and No Distracter (none) condition. We want to first contrast both distracter conditions with the no distracter conditions, and then contrast the results with each other: (Negative > None) >
by
aojha17
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AFNI Message Board
Hi there,
I'm looking to calculate tSNR values and have used the following syntax, as per this post:
3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc"[$ktrs]"
3dTstat -stdev -prefix rm.noise.all errts.${subj}_REML+tlrc"[$ktrs]"
3dcalc -a rm.signal.all+tlrc
-b rm.noise.all+tlrc
by
aojha17
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AFNI Message Board
Hi Gang,
Thanks for bearing with me. Here's a new error when I fixed the model specification:
Error in checkForRemoteErrors(val) :
11 nodes produced errors; first error: missing value where TRUE/FALSE needed
Calls: aperm ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Execution halted
Amar
by
aojha17
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AFNI Message Board
Hi Gang,
That got rid of the error regarding 'xinit' but I'm still getting the earlier error that the model test failed, despite now including everyone and using different label specifications. I'm including the full script below. Thank you for your help!!
Amar
3dLMEr -prefix 3DLMER_EFNBACK -jobs 12 \
#-mask EmoVNeu_Thresh_resamp_binary.nii \
-model 'emotion
by
aojha17
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AFNI Message Board
Hi Gang,
I'm now getting an error that says "object 'xinit' not found"—I installed "lmerTest," "snow," and "phia." I see someone else had the same problem but don't see a solution to it. I didn't see 'xinit' in the 3dLMEr script itself but did in the 3dLMERr.R script... Any help, as always, is greatly appreciated!
A
by
aojha17
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AFNI Message Board
Hi Gang,
Thanks for the reply! I'm still having some trouble ("model test failed"). I'm working with a miniature version of the final script for debugging purposes, posted here:
3dLMEr -prefix EFNBACK_LMER_mini2 -jobs 12 \
-model 'emotion*group+site(1|Subj)' \
-bounds -2 2 \
-gltCode p-d 'group : 1*p -1*d emotion : 1*pos' \
-gltCode p-d 'grou
by
aojha17
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AFNI Message Board
Hi Gang,
Thank you for your work on this. We'd like to use 3dLMEr to test functional activation differences between groups during an emotional faces task. There are three groups (ADHD-P, ADHD-D, and ADHD-NA), three emotional trial conditions (pos, neg, neut), and a few covariates we want to include in our model (age, sex, handedness, site, and co-morbidities). Basically, we want to test d
by
aojha17
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AFNI Message Board