We are switching to Freesurfer for surface-based analysis of task fMRI data (after fMRIprep preprocessing), and have hit a question that doesn’t seem to be addressed in the tutorials.
We have 3 functional runs per subject. They are not longitudinal (all collected the same day, accompanied by one T1). These runs are all the same task but don’t have identical timecourses (conditions appear in different order each run). How do analyze data of this structure?
For example, in FSL you perform a fixed-effects analysis across the 3 sessions to create a second-level “participant average” result, which serves as input to a third-level “across participants” analysis.
I can think of ways we could address this (e.g. concatenate data and timecourses across sessions before first-level analysis), but I’d love to know what is the correct way!