Hello afni experts,

I have a question regarding the use of -Rerrts output from 3dremlfit for resting state data. I should first mention that I am analyzing resting state data but instead of looking at functional connectivity I want to investigate if BOLD signal variability (calculated with the MSSD measure) increases after an intervention. So the actual amount of variability in the remaining residuals is very important for my analysis.
I read on this message board that it is not recommended to use prewhitening in resting state because the autocorrelation in the remaining residuals is assumed to be related to neural activity so we don t want to whiten the residuals. My question is: What is your opinion about using the unwhitened residuals (the output of the -Rerrts option) from 3dremlfit instead of the residuals from 3dDeconvolve?

The reason why I am asking is because of a paper by Molly Bright that caught my attention: “Potential pitfalls when denoising resting state fMRI data using nuisance regression”. She argues that also in resting state the fitting procedure should include an estimate of the autocorrelation in the residuals and account for this during the fit to achieve valid statistical inference.

So I would like to use the remaining unwhitened residuals from 3dremlfit instead of the residuals from 3dDeconvolve assuming they will be more accurate? When I look at some of my data, the remaining residuals from 3dDeconvolve and the output from remlfit -Rerrts do seem to differ. I am just wondering what you guys think and if this is something that could potentially make a difference for my type of analysis (BOLD signal variability -MSSD).

Thank you very much in advance for any thoughts!
Carolin