Magnetic resonance imaging (MRI) permits in vivo quantification of brain compartment volume, and has many applications in cognitive, clinical and comparative neuroscience. There dre numerous approaches for obtaining a brain volume estimate from MRI, and the primary focus of this paper is to provide an overview of the methods available to estimate the volume of three brain structures that are of particular interest in the neurosciences: the cerebral hemispheres, hippocampus and Brocas area. We provide information on choice of computer software, hardware compatibility, required user expertise, the application of manual and automated MR image analysis techniques, and anatomical guidelines, providing the reader with enough information to decide on their approach at the outset of a quantitative MRI study. We advocate the use ofstereology in conjunction with point counting for an unbiased and time efficient estimate of brain compartment volume.
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