Hi! Apologies if this is a very simple thing to do. I’m hoping to find measurements of the distance of layer 5 from the pial surface as well as the pial surface area in primary somatosensory, visual and auditory cortices. I can see layer 5 and can select the areas in the interactive atlas viewer, but I’m not sure how to take measurements. Any help would be greatly appreciated!
Hello, this is a great question. Because the cortex is a curved surface, the distance measurements have to be done using a curved path rather than a straight line. In Wang et al. (2020), we developed a set of curvilinear coordinates (‘streamlines’) that represent the shortest distance paths from the meningeal to pial surfaces. These precomputed streamlines are available here: Data Files — ccf_streamlines 1.1.4 documentation, see cortical_layers_10_v2.h5.
This array contains the thickness of each layer for each streamline. Streamlines will need to be aggregated by structure and averaged to get the average layer depth for the entire region.
Visual cortex is a special case because the average layer depths were used for normalization. The average layer depths have already been precomputed for visual cortex and can be found in the avg_layer_depths.json file.
For pial surface area, you could aggregate using the pial surface points for streamlines or use the 2D flatmap representation, flatmap_dorsal, which is a 2D projection of the cortical surface. Because of the intrinsic curved geometry, the 2D and 3D calculations of the pial surface may differ slightly, but it’s the easiest way to getting a close estimate.