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Mindboggling morphometry of human brains

Fig 2

FreeSurfer and ANTs gray/white matter segmentation.

Left: Coronal slice of a T1-weighted brain MRI. Middle: Cross-section of FreeSurfer inner (magenta) and outer (green) cortical surfaces overlaid on top of the same slice. The red ellipse circumscribes a region where the FreeSurfer surface reconstruction failed to include gray matter on the periphery of the brain. Right: Cross-section of ANTs segmentation. The blue ellipse circumscribes a region where the ANTs segmentation failed to segment white matter within a gyrus that the FreeSurfer correctly segmented (compare with the middle panel). The purple box in the lower right highlights a region outside of the brain that the ANTs segmentation mistakenly includes as gray matter. To reconcile some of these discrepancies, Mindboggle currently includes an optional processing step that combines the segmentations from FreeSurfer and ANTs. This step essentially overlays the white matter volume enclosed by the magenta surface in the middle panel atop the gray/white segmented volume in the right panel.

Fig 2