That error message is so peculiar. Without access to the data, I cannot make sense out of it. Let us know if you could get it resolved.by

> it seems to try to open some window, so that it needs xinit? In that case, is there an option in 3dLMEr to supress any plots popping up? Is this behavior reproducible? I cannot think of anything in 3dLMEr that requires X server.by

Phoebe, what is your AFNI version? afni -ver You may have to update your AFNI. Also, use multiple CPUs with the -jobs option if possible.by

> I am using R version 4.01.1, so my R library is /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib > any chance I can get AFNI's R_io.so to work with it? Greetings, Chairman Z- Rick is trying to build an R_io.so for Mac OS 10.15, and hopefully it will be available soon. In the meantime, if you're in a hurry, get R 3.6.3 (https://cloud.r-project.org/bin/by

Sojung, it's up to you which method you want to pursue. > functional connectivity is the correlation of BOLD signals between the ROI and the whole brain. The averaged BOLD > time series of all voxels in the ROI is compared against each voxel in the brain, and clusters of voxels that correlate > highly enough to be significant. This would be a Seed-to-Voxel analysis. Your defby

Could you show the contingency table about Task and Gender? You can find it on the terminal when you run your 3dLME script. The empty space after the positive (+) and negative sign (-) should be removed in your original script: -gltLabel 4 'efnback_vs_rest' -gltCode 4 'Task : 1*efnback1 + 1*efnback2 - 2*rest' \ -gltLabel 5 'dynface_vs_rest' -gltCode 5 'Taby

Florin, I don't have much experience with causality analysis of FMRI data, so I cannot make general recommendation about the methodology. It would be interesting if you could gain some insight out of 3dGC.by

> I have installed the packages to my personal library, but would this be causing some problem with reading the packages? It's fine: the installed R package would only be accessible to you, but not to others who share the server. However, you need to first install R 3.6, and then you may have to re-install all the required R packages.by

Dani, What OS are you running on? What is the R version? If it's R version 4.0, there might have some thorny issue we need to sort out, and you may have to use version 3.6 to get around the issue.by

> I want to calculate the anger+fear activation map but I am confused how to average this Do you get the average effect between anger and fear at the subject or population level? At the subject level, if you just want to get the effect estimate, do 3dcalc -a anger -b fear -expr “a+b” -prefix ... If you want to get both the average effect and its statistical evidence, you would have toby

Amy, Try the following: cd /Library/Frameworks/R.framework/Versions rm -rf 3.5 Then download R 3.6.3 fromby

Florin, I don't feel comfortable enough to recommend the modeling approach implemented 3dGC even though I wrote the program more than 10 years ago. As for PPI, check out the following video: Another possibility is to model the effect associated with each occurrence of high/low word, and perform what is called beta series analysis in the literature.by

> A suggested future addition, to make this more straightforward, is to have a 3dLM version of 3dLMEr (or even better, allow robust linear modeling as well). In fact 3dMVM does allow voxel-wise covariate, but the limitation is that currently it can only take one voxel-wise covariate (you have two in this case). And it also does robust regression. > For 2) Remove the population mean ofby

I assume x and y each has one value per subject. See if the following works for you. 1) Remove the population mean of x from each subject and call it X; 2) Remove the population mean of 'brain' at the voxel level and call it BRAIN; 3) Obtain the product of X and BRAIN using 3dcalc for each subject and call it XB: 3dcalc -a BRAIN -expr 'a*x' -prefix XB 4) Createby

Hi Dante, Everything in the time series regression model is partial because they all share the same plate of food (i.e., data). In other words, it is not like one regressor walks into the kitchen first and takes as much as it wants; rather, they all split everything at the same time in an impartial fashion even though each one gets a partial proportion.by

Anthony, I assume that "brain" is a 3D dataset for each subject. Could you explain what are "x" and "y"?by

Juliann, > I re-coded the six factors as you suggested (i.e., -1 and 1 rather than 0 and 1), but I got the same error that the model does not pass the test voxel. Did you add the 6 variables of Scanner, AA, Male, BinCan, BinTC, and BinDrug to part of quantitative variable through option -qVars? If not, it would not work as intended. > Is there a command I could add to my script thaby

Youn, > Would it be possible to conduct a Task-related functional connectivity analysis with AFNI? Unfortunately "functional connectivity" is a flashy but murky and imprecise term, and I have no idea what it exactly means in terms of modeling specifics. You mentioned ROI and trial-level analysis, but could you describe a little bit more in details as to what you'd like toby

> 3dREMLfit is the ideal option because fMRI time series are temporally autocorrelated The reason is not that FMRI time series are temporally autocorrelated. Rather, we currently cannot explain everything embedded in the FMRI data, thus the resulting residuals still contain some extent of temporal structure. > I use the -iresp command in 3dDeconvolve to model my HDR No, the optionby

Hmm... it seems those contingency tables only show the associations of each subject with those 6 factors, and they do not include the most informative ones about the those 6 factors: Scanner, AA, Male, BinCan, BinTC, BinDrug. I suspect that the problem is that you don't have all the combinations available among those 6 factors. 3dMVM is picky in the sense in the sense that it requires allby

Hi anonymous, if the question whets your appetite, the answer is only a click away.by

Just as subjects are samples from a hypothetical population pool, so trials in an FMRI experiment are instantiations from a condition category. If cross-subject variability should be properly accounted for, why would cross-trial variability not be on an equal footing? In addition to improving generalizability, capturing trial-level effects may also gain estimation accuracy and statistical sensitiby

Juliann, You have 6 subject-grouping factors: Scanner, AA, Male, BinCan, BinTC, BinDrug Could you show the contingency tables about these 6 factors? You can find them before the error message.by

Phoebe, Sub-brick #2 is not p-value, but correlation coefficient instead. Are you trying to perform Fisher Z-transformation? If so, do 3dcalc -a delay+orig'[2]' -expr 'log((1+a)/(1-a))/2' -prefix zscore or 3dcalc -a delay+orig'[2]' -expr 'atanh(a)' -prefix zscoreby

Ana, what is the motivation for such subdivision? Divide them based on what: different correlation ranges/intervals?by

Phoebe, What kind of values do you have in the sub-brick #2 of the file delay+orig? Could you share the output of the following command? 3dinfo delay+orig'[2]'by

The statistical evidence is intrinsically continuous, so why would we have to stick to a specific cutoff value? The sphericity assumption could be violated, leading to inflated F-statistics. On the other hand, the false assumption of no common information shared across the brain results in inefficient modeling with the mass univariate approach, and excessively penalizes the statistical evidence.by

When you have a within-subject (or repeated-measures) factor with at least three levels, you could use the option -SC to apply Mauchly's adjustment.by

You don't have to run this analysis with the ROI. Instead, just apply the ROI mask directly to the output from your previous analysis. The mask problem will hopefully be fixed in the next AFNI official release.by

SEM is generally considered as a model validation approach. I'm not an expert on SEM and don't have a clear answer about this: it seems a little controversial to use it for model search.by