Keywords: Segmentation, AnimalsBrain extraction in an MRI image is the first pre-processing step of a neuroimaging quantification pipeline. Once the brain is extracted, further post-processing becomes faster, more specific, and easier to implement and interpret. Existing brain extraction tools are mostly adapted to work on the human anatomy, or on specific animal species. This gives poor results when applied to animal brain images. We developed an atlas-based Veterinary Images Brain Extraction (VIBE) algorithm that is fully automatized and was successfully tested on different cats and dogs breeds, 3D and 2D MRI images, different contrasts (T1-weighted, T2-weighted and T2 FLAIR) and acquisition planes.
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