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.　Microsc.　Res.　Tech.　76:　7-11,　2013.　(C)　2012　Wiley　Periodicals,　Inc.