I’m an fMRI beginner and I have a very basic mathematical question about what 3dDeconvolve does and does not include in each GLM. I consulted with a good friend who has used AFNI for years, but he wasn’t sure so I thought I would inquire here.
I am using a block design with six conditions. My timing files for each condition include all the TRs that occur during that condition, but there are a few TRs after each block that are not represented in any of the timing files.
My question: When I get my coefficients for each contrast (e.g., conditionA_vs_conditionB), do those GLMs include the unmodeled TRs in any way (e.g., are they modeled as “rest” and/or effectively covaried out)? Or are data from unmodeled TRs entirely excluded from analysis?
Similarly, I know my “conditionA_vs_conditionB” contrast includes regressors for covariates of non-interest (e.g., motion). Are the data from the other conditions (e.g., conditions C, D, E, F in this example, and/or rest) accounted for in the GLM in any way?
I think these questions both boil down to: How do I know what else is being statistically controlled in the GLM?
Thanks so much!