Measurement of brain volume using MRI: software, techniques, choices and prerequisites

Magnetic resonance imaging (MRI) permits in vivo quantification of brain compartment volume, and has many applications in cognitive, clinical and comparative neuroscience. There are 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 Broca’s 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 of stereology in conjunction with point counting for an unbiased and time efficient estimate of brain compartment volume.