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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
I don't see any obvious problems with your script. What is your AFNI version?
afni -ver
Unrelated to the error message, the following line
-glfLabel 1 'GroupByTime' -glfCode 1 'group : 1*ctrl -1*pat cond : 1*v1 -1*v2' \
could be changed to
-gltLabel 9 'GroupByTime' -gltCode 9 'group : 1*ctrl -1*pat cond : 1*v1 -1*v2' \
by
gang
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AFNI Message Board
Yes, those 3 lines would help you parse the age effect in terms of its directionality.
by
gang
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AFNI Message Board
Change the following line
-qVars "age+sex+educ+movement" \
to
-qVars "age,sex,educ,movement" \
by
gang
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AFNI Message Board
Dante,
For your second analysis, I assume that you're interested in the cross-brain correlation with the seed, not the scaling factors relative to the response at the second. So, would it better to use the Fisher-transformed correlation values from each subject as input for population-level analysis? That way, your effect magnitude at the population level would be directly related to corr
by
gang
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AFNI Message Board
Dante, what is the metric you used as input for 3dLME: Fisher-transformed correlation, BOLD response, or something else?
by
gang
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AFNI Message Board
> One rationale backing the current approach might be that we first need to regress out the (possibly existing) signals
> imposed by the driving input in order to generate data composed of pure noise.
I'm not so familiar with the implementation, but I suspect that is likely the rationale. I wonder how to flip the sign with the observed data (rather than the residuals) when one or m
by
gang
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AFNI Message Board
Carole,
3dICC is designed to estimate ICC when an effect/measurement is obtained two or more times (like sessions in fMRI scanning) among subjects. What is the repetition variable in your case? Could you describe your data structure?
by
gang
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AFNI Message Board
Bryna,
Thanks for reporting the issue. Put the following file into your AFNI binary directory (e.g., ~/abin/):
and then try running your RBA script again. Let us know if this fixes the problem. The fix will be also in the next AFNI official release.
by
gang
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AFNI Message Board
What is your AFNI version?
afni -ver
Consider updating your AFNI:
@update.afni.binaries -d
and try running 3dLME again.
by
gang
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AFNI Message Board
This issue appears be caused by all the input files containing only zero values.
by
gang
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AFNI Message Board
Put the following two files into your AFNI binary directory (e.g., ~/abin):
See if these updates would fix the problem. These updates will be also in the next official release.
by
gang
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AFNI Message Board
Milena,
Other considerations (e.g., causal inference) aside, the full model is appropriate if the interaction effect 'BC' is substantial. Among the three individual models, the last one "-model 'Age+DaysDrk+Task*Sex*Time*BC'" is problematic because the main effects of binge drinking and craving are not properly accounted for. The other two models assume the absenc
by
gang
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AFNI Message Board
> Do I use 0.71478 5.91395 9.13712 in the 3dClustsim?
Yes, I believe that's correct. The first three numbers are the (a,b,c)-parameters from the ACF expression, and the last number (13.7085) is the effective FWHM.
by
gang
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AFNI Message Board
Nuttaon,
The output from 3dFWHMx -acf should have 4 columns. What is your AFNI version?
afni -ver
Try updating your AFNI if your version is too old:
@update.afni.binaries -d
by
gang
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AFNI Message Board
Milena,
> was wondering whether it would have been better to just center both variables outside of 3dlme, then just
> multiply the two to get BC, and then enter centered percHDD, cravP and the two multiplied (i.e., BC) in the
> data table while listing zeroes under qVarCenters for all three variables (CravP, percHDD and BC)?
Yes, it makes more sense to manually center both variab
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gang
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AFNI Message Board
> I had seen that we could average the <3dFWHM errts*> output values across subjects to use as the smoothing parameter
> in 3dClustSim. Is that what one would do in the case of ACF (i.e., average each of the values in the output of 3dFWHMx)?
Some extent of arbitrariness is involved here. In addition to the averaging approach, another conventional method is to obtain the population
by
gang
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AFNI Message Board
> I'm using afni 22.1.14
Tien, could you update your AFNI and see if the most recent version would fix the issue?
@update.afni.binaries -d
by
gang
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AFNI Message Board
Hmm... imagine sipping Paulaner... I'll try to figure out whether there is an automatic way to pinpoint such an issue.
by
gang
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AFNI Message Board
You may need to check your vision The following line
s4 s11Correlation_Subject4_Subject11+tlrc \
should be
s4 s11 Correlation_Subject4_Subject11+tlrc \
As for the following message, you can turn a blind eye:
updating R_LD_LIBRARY_PATH ...
by
gang
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AFNI Message Board
> What I would like to know is if the activation in the regions that appear to predict craving during stress in males (or females)
> may be stronger among those males (or females) with higher % of binge drinking days (i.e., this relationship between stress
> and craving in males may vary as a result of heavy drinking days)
If I understand it accurately, you're interested in the
by
gang
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AFNI Message Board
> I'm looking to set up a 3lme with two covariates of interest that are continuous variables.
The following two lines are not semantically meaningful:
-gltLabel 1 'Male_stress_HDD_CravP' -gltCode 1 'Gender : 1*Male Task : 1*stress percHDD : CravP : ' \
-gltLabel 2 'Male_drug_HDD_CravP' -gltCode 2 'Gender : 1*Male Task : 1*drug percHDD : CravP :
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gang
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AFNI Message Board
> When running 3dMVM using a script that runs successfully under afni 20.3.03, I get the following error on the virtual machine running AFNI 22.2.03
The error message is likely due to a recent change in a newer version of R. Try updating your AFNI to the most recent version.
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gang
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AFNI Message Board
Two approaches:
1) Conventional method: use 3dHWHMx -acf to estimate the spatial smoothness and then obtain the cluster size based on 3dClustSim
2) Highlight-but-not-hide: see following discussions
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gang
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AFNI Message Board
Maria, do you mind sharing the error message so that I could have a better sense about what's going on?
My suspicion is that you code the "run" column with square brackets in the labels. However, in your "glt" and "glf" coding, the square brackets are not used. I would drop the square brackets in the "run" column.
A side note: those 6 "glf&q
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gang
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AFNI Message Board
Maria, you need to use -bsVars and -wsVars to specify the variable type for "group" and "run".
by
gang
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AFNI Message Board
Removing outliers can be problematic due to the arbitrariness involved. A more principled way is to handle it through the modeling process. If you obtain the contrast between the two conditions for each subject, you can try robust regression by feeding the contrast together with the covariate to 3dMVM with its option -robust
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gang
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AFNI Message Board
> Does AFNI now have ICA for both pre-processing AND for analysis?
3dICA.R is just a simple tool for spatial ICA as shown on the web page you linked. Unfortunately there has been no further development.
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gang
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AFNI Message Board
> I do have some missing data that I would potentially like to incorporate, so I am still interested in this analysis using 3dlme.
In that case, 3dLME or 3dLMEr would be a better choice.
> However, I am curious why you would generally suggest 3dMVM instead of 3dLME?
3dMVM would be more suited for a factorial structure with within-subject factors. For example, with two or more with
by
gang
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AFNI Message Board