Fig. 7: Manual segmentation method for primate brains.
a A schematic representation of the manual segmentation pipeline. T1- and T2-weighed (T1w and T2w) MRI scans previously described in Heuer et al.89 were used to make initial cerebellar masks by subtracting cerebral masks from whole brain masks with StereotaxicRAMON. Some initial cerebellar masks were made through local thresholding and interpolation with Thresholdmann. Cerebellar masks were then uploaded to BrainBox for manual segmentation. Manual segmentation was performed iteratively with interpolation between slices through mathematical morphology operations, until segmentations reached satisfactory quality. Volumes were then downloaded with a custom python script for subsequent analysis in R. b–c Example segmentations in stereotaxic planes for the cerebellum and ansiform in the hamadryas baboon. b Cerebellar segmentations primarily involved removal of the brain stem, removing erroneously marked tissue and fissures, and reconstructing damaged tissue. c Ansiform segmentations additionally involved identification of superior posterior and ansoparamedian fissures, and segmentation between these. Segmentations were made so they did not enter vermal portions of lobule VII. Example masks are color-coded (see legend), but the meaning of the colors themselves is arbitrary. Scale bars are provided for each image.
