Boundary lines of the gray matter (GM) ribbon to cerebrospinal fluid (CSF) and white matter (WM) were estimated with FreeSurfer (v6.0) (Fischl 2012) from whole-brain 0.7mm MP2RAGE data that had been acquired in previous studies and were registered here to the functional EPI space using ANTS (Avants et al. 2008). These boundaries were used as visual guidance to manually segment GM in EPI space slice-by-slice, as described in the manual (https://layerfmri.com/getting-layers-in-epi-space). A coordinate system across cortical layers and columnar structures was estimated in LAYNII (https://github.com/layerfMRI/LAYNII). LAYNII is an open source C++ software suite for computing layer and column functions. We estimated the depth of equidistantly distributed layers1. With the resolution of 0.8 mm, we obtained 4–6 independent data points across the thickness of the cortex. Across these data points, we created 20 layers2 across the thickness of the cortex on a 4-fold finer grid than the effective resolution. The entire pipeline of this analysis is described here: https://layerfmri.com/analysispipeline. Cortical ‘columnar’ structures were also determined in LAYNII’s LN_3DCOLUMN program with the following algorithm: For each voxel, the next closest (Euclidean distance)
