Dear FSL experts,
I am running a resting state fMRI analysis in which we will regress out the time series from regions of no interest (white matter etc.), and then apply several ROIs of interest to the residuals to get time series information. I found a website (unrelated to you) describing how to do this in FSL, and they suggested turning on intensity normalization and turning off prewhitening to get the residuals. Looking at the descriptions you provide in the gui help, I don't see why this would be the case, but wanted to check with you experts before I proceeded. My TR is 2.1 s. Is there some reason specific to getting residuals for rs-fMRI that I'd want to turn on intensity normalization and turn off prewhitening, or is this likely just a preference of the lab that posted the instructions?
Also, it looks like the lab that posted the website instructions normalizes the residuals after they are obtained. Is this a necessary step before using fslmeants to get the time series information, or does this depend on whether prewhitening is used?
Thank you for your advice & help.
Meredith
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