MultipleRuns

What to do with multiple runs or multiple sessions?

First of all, all preprocessing steps can be done across all runs. Runs are acquired in the same session, therefore in the same timespan with similar head positions. All runs need to be corrected in the same manner in the following way: First, realign (estimate) the runs to one of their run-specific functional scans (first or middle), then slice-time correct all functional runs, next realign the functional runs to one chosen functional scan (first or middle) and finally get the mean across functional runs and realign all accordingly. In the next step, one can coregister, estimate only, the anatomical scan to the functional mean. Then normalize (estimate) the coregistered anatomical to an MNI template and write all functional runs to MNI space, using the estimated parameters. In the last step, one can smooth across all runs (Thompson, 2013).

Thompson, R. (2013). Principles of analysis. MRC CBU Imaging Wiki. https://imaging.mrc-cbu.cam.ac.uk/imaging/AnalysisPrinciples