Calculation of dice scores

Dice score is the indicator for quantifying the accuracy of segmentation and can be calculated as:

where A is the ground truth of segmentation, while B is the result by brain-map. A∩B represents the number of pixels where A and B overlap, and A+B refers to the total number of pixels in A and B.

Here, with referring to BrainsMapi (Ni et al., 2020) methods, we compared the registration/segmentation results by four registration tools at both coarse region level and fine nuclei level. As we assessed the accuracy of these methods at brain-region level, 10 brain regions, Outline, CB, CP, HB (hindbrain), HIP, HY (hypothalamus), Isocortex, MB (midbrain), OLF, and TH (thalamus), were first selected from the entire brain for comparison. Then we further picked out 50 planes in each selected brain region (totally 500 planes for 10 regions) and manually segmented them to generate the reference results (ground truth). For nuclei-level comparison, we selected nine small sub-regions, ACA, ENT, MV, PAG, RT, SSp, SUB, VISp, and VMH as targets, and performed similar operation on them with selecting five representative coronal sections for each region. To allow the manual segmentation as objective as possible, two skillful persons independently repeated the abovementioned process for five times, and a STAPLE algorithm (Warfield et al., 2004) was used to fuse the 10 manual segmentation results to obtain the final averaged output as the ground-truth segmentation, for each region.