Automatic segmentation of the brain and intracranial cerebrospinal fluid in T1-weighted volume MRI scans of the head, and its application to serial cerebral and intracranial volumetry

A new fully automatic algorithm for the segmentation of the brain and total intracranial cerebrospinal fluid (CSF) from T1‐weighted volume MRI scans of the head, called Exbrain v.2, is described. The algorithm was developed in the context of serial intracranial volumetry. A brain mask obtained using a previous version of the algorithm forms the basis of the CSF segmentation. Improved brain segmentation is then obtained by iterative tracking of the brain–CSF interface. Gray matter (GM), white matter (WM), and intracranial CSF volumes and probability maps are calculated based on a model of intensity probability distribution (IPD) that includes two partial volume classes: GM‐CSF and GM‐WM. Accuracy was assessed using the Montreal Neurological Institute's (MNI) digital phantom scan. Reproducibility was assessed using scan pairs from 24 controls and 10 patients with epilepsy. Segmentation overlap with the gold standard was 98% for the brain and 95%, 96%, and 97% for the GM, WM, and total intracranial contents, respectively; CSF overlap was 86%. In the controls, the Bland and Altman coefficient of reliability (CR) was 35.2 cm3 for the total brain volume (TBV) and 29.0 cm3 for the intracranial volume (ICV). Scan‐matching reduced CR to 25.2 cm3 and 17.1 cm3 for the TBV and ICV, respectively. For the patients, similar CR values were obtained for the ICV. Magn Reson Med 49:872–884, 2003. © 2003 Wiley‐Liss, Inc.