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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
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Thanks for the response Gang.
Do you know of a good resources that explains in detail how to setup the different models using the coding scheme in 3dLME. I realize that R is being used to do some of the model testing. Is there an R function in 3dLME that provides more documentation on how to properly code up different linear models?
by
sgreen
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AFNI Message Board
Hey Gang,
Its just the standard error when the model fails.
~~~~~~~~~~~~~~~~~~~ Model test failed ~~~~~~~~~~~~~~~~~~~
Possible reasons:
0) Make sure that R packages nlme and phia have been installed. See the 3dLME
help documentation for more details.
1) Inappropriate model specification with options -model, or -qVars.
2) In correct specifications in general linear test codin
by
sgreen
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AFNI Message Board
Hello AFNI team,
Trying to analyze some data with a condition factor and between subject covariate. Just want to see what effect condition, covariate and interaction between them effect brain responding.
The model runs without incident when I don't include any contrasts.
3dLME -prefix $outPath -jobs 20 \
-mask grpMask+tlrc \
-model 'cond*lftm' \
-q
by
sgreen
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AFNI Message Board
Hey Gang,
Thanks for the response. I'm surprised that I should treat a quantitative score of symptom severity as a between subject factor since its not a group factor. Perhaps there is a confusion because I am currently only running the analysis on a subset of data just to learn how to 3dMVM. The full data set will have 40 subjects with symptom severity scores ranging anywhere between 0 t
by
sgreen
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AFNI Message Board
Trying to use 3dMVM to show the effect of a covariate (symptom severity) on a within subject factor (3 levels). Unfortunately I can't figure out how to set up the model and test for this effect. My best guess is pasted below but it returns the error:
** Error:
Failed at GLT No. 1! Make sure that the model or GLT specification syntax is correct.
I can't for the life of me figur
by
sgreen
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AFNI Message Board
Hey Rick,
We have a quick questions about calling detrend in 3dFWHMx.
First, since afni_proc already detrends we figured the residuals would already be detrended. Would you expect running detrend with 3dFWHMx on residuals to have considerable impact since they should have already been detrended by afni_proc.
Second, since afni_proc detrends for each run could some of the differences we a
by
sgreen
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AFNI Message Board
Hello,
I have some questions regarding the new option -acf both for 3dFWHMx and 3dClustSim. To estimate the blurring across all subjects to determine acceptable cluster size at .005, I ran 3dFWHMx on each subject’s residuals (errts+tlrc). I averaged the three parameters across subjects to get the mean radius (r) and two fitted parameters (a & b). I entered these parameters into the 3dClus
by
sgreen
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AFNI Message Board
Hello AFNI team,
I'm currently running an analysis and I have ran into a problem. During registration afni_proc executes 3dAllineate looking for a file called warp.all.anat.aff12.1D. Unfortunately this file has not been created so the afni_proc script crashes. I was wondering if anyone knows what preceding part of the afni_proc generates this file and why it may not have been generated
by
sgreen
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AFNI Message Board