Software - Multiple Atlas Hippocampus And Ventricle Extraction (HCV)

This is a fully automated multiple atlas hippocampus and ventricle extraction application that works on T1 images. The hippocampal segmentation is done according to the Harmonized Hippocampal Protocol (HarP). A pre defined set of 100 atlases is taken and each atlas is rigidly, then affinely registered to the image of interest. Then using diffeomorphic demons, non-rigid registration is performed to the target image. The resulting non-rigid transform is then used to warp the "HarP" hippocampii masks defined on the atlas to the image of interest space. Then atlas fusion is done as per the weight of each atlas according to its local similarity with the target image referred to as MALF. Next steps refine and pool the labels using the information from the three tissue segmentation. Final outcome is the hippocampal mask.

Figure Multi-Atlas Hippocampus Extraction Flowchart.

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