Software packages for neuroimage processing

Abstract

This chapter provides an overview of software packages commonly used within the neuroimaging community. The primary focus is on software for the analysis of structural and functional magnetic resonance imaging (MRI) brain data, although the software summarized may be extensible to other neuroimaging modalities such as computed tomography (CT) and positron emission tomography (PET). The breadth of available software and its features are substantial and cannot possibly be covered in a single chapter. Instead, this chapter is meant to serve as a software guide for clinicians who are inclined to utilize neuroimaging methodologies in their own research.

Neuroimaging software may address a number of components of the image analysis pipeline. These include preprocessing, processing, and postprocessing. In this chapter, image preprocessing refers to methods typically employed to prepare images for analysis (eg, noise filtering, motion correction, brain extraction, etc.). Image processing refers to methods that extract, interrogate, manipulate, and formulate the image to arrive at a result for interpretation. Image postprocessing refers to methods that operate on the processed image to better represent the results of the processing (eg, surface rendering, image overlay, image tiling, histograms, etc.). A discussion of these methodologies is outside of the scope of this chapter.