Introduction

Using the basic installation of nordicICE one may segment regions of images based on their pixel intensity (See <Segmentation analysis > . This section describes the additional brain extraction features included in the Brain Extraction module.

Brain extraction refers to the process of removing non-brain tissue in an image series. The goal is to reduce the original series to a series in which only brain tissue is left.

Various methods for brain extraction are available in different software packages. These methods vary among others in the amount of user interface required to give a reasonable brain extraction. nordicICE 's segmentation module includes an implementation relying on a method published by Stephen M. Smith in Human Brain Mapping 17:143-155(2002). This method fits a deformable tessellated mesh onto the surface of the brain in an iterative manner. The method is not intended to segment the surface at the finest level. Sulci and gyri are in general too small to be visualized by this method. The method requires little user interaction and may in most cases be run with the default parameters.