To enable the analysis of laminar fMRI, we need to align the fMRI volumes to those intermediate laminar surfaces. Apparently, the gray/white matter boundary in the EPI volume is easily identified automatically. We employed a method called boundary-based registration (BBR) [85]. It identified the interface between gray matter and white matter in the EPI data and then calculated a 12 degrees of freedom affine transformation, which registers the interface in EPI data to the corresponding surface reconstruction from the anatomical data (Fig. 2). After the registration, the results were visually inspected for each subject and manually edited, if needed [85].
