A template-based automatic skull-stripping approach for mouse brain MR microscopy.

Small animal magnetic resonance microscopy (MRM) has been widely used today in computational neuroanatomy. Accurate identification of brain tissue in a mouse MRM is a critical fundamental step in neuroimaging processing, which is given less attention. This study presents an automatic skull-stripping technique based on template models and histogram analysis. Results were evaluated by calculating the Jaccard similarity index (JSI) and boundary concordance ratio (BCR) between the automatically segmented and manually traced brain volumes. Results demonstrate that this technique accurately extracts the brain volume (mean JSI = 97.1%, BC = 94.4%). The brain extraction method presented in this study will greatly facilitate analysis of neuroimaging studies of rodent animals in neurodegenerative diseases.