I am planning on running a group analysis to determine whether there is greater BOLD activation in group A vs group B for different trial types. I plan to fit a GLM to get beta weights for each subject for the following contrasts: 1. trial 1 vs rest, 2. trial 2 vs rest, 3. trial 1 vs trial 2. Then I plan to test the group differences with 3dttest++ to see whether the main hypothesis that there are greater beta values for contrast 2 in group A compared to group B. My questions are as follows:
- Is any thresholding applied to the first level analysis (besides potentially brain masking) or are all Beta values from an individual subject input into the second level analysis?
- Is this thresholding procedure the same for most software packages or unique to afni?
- Finally are the group labels permuted with the -clustsim option or something else (I saw previous posts mention the contrast weights were flipped but I wasn’t sure what this means or if this was the current method)?
Thanks for the help!