Brain Extraction

Accurate and Robust Extraction of Brain Regions using a Deformable Model Based on Radial Basis Functions


Brain extraction from head magnetic resonance (MR) images is a classification problem of segmenting image volumes into brain and non-brain regions. It is a difficult task due to the convoluted brain surface and the inapparent brain/non-brain boundaries in images.

This paper presents an automated, robust, and accurate brain extraction method which utilizes a new implicit deformable model to well represent brain contours and to segment brain regions from MR images. This model is described by a set of Wendland’s radial basis functions (RBFs) and has the advantages of compact support property and low computational complexity. Driven by the internal force for imposing the smoothness constraint and the external force for considering the intensity contrast across boundaries, the deformable model of a brain contour can efficiently evolve from its initial state toward its target by iteratively updating the RBF locations.

In the proposed method, brain contours are separately determined on 2D coronal and sagittal slices. The results from these two views are generally complementary and are thus integrated to obtain a complete 3D brain volume. The proposed method was compared to four existing methods, Brain Surface Extractor, Brain Extraction Tool, Hybrid Watershed Algorithm, and Model-based Level Set, by using two sets of MR images as well as manual segmentation results obtained from the Internet Brain Segmentation Repository. Our experimental results demonstrated that the proposed approach outperformed these four methods when jointly considering extraction accuracy and robustness.


Figure : . Flowchart of the proposed method. (a) The effective intensity range [t1, t2] and a rough head/background threshold t are estimated from the intensity histogram. (b) Then the voxels with intensity value within [t, t2] are used to approximate the brain centroid. (c) Applying DOG operator with zero threshold, the global WM intensity tw and CSF intensity tc are decided from the voxels within the ellipsoid approximating the brain shape. The brain areas of the (d) coronal slices and (e) sagittal slices are extracted. (f) A complete 3D brain region is determined from the complementary areas segmented from two different views.