FreeSurfer Beginners Guide

FreeSurfer is a versatile set of software tools that will help you analyze structural and functional MRI data of the brain. It is comprised of several components -- user interfaces, graphical displays, and executable commands.

FreeSurfer provides many anatomical analysis tools, including: representation of the cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from the rest of the brain, skull stripping, B1 bias field correction, nonlinear registration of the cortical surface of an individual with an sterotaxic atlas, labeling of regions of the cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.

A handy overview of the major processing steps taking place in a standard FreeSurfer workflow are described in this PDF slide presentation: [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/FSL_anatomical_stream.pdf Building Anatomical Models with Freesurfer].

MRI Parameters

FreeSurfer requires that the MRI data conform to certain parameters. The slice thickness should be 1.3mm and the Field of View should be 256mm. To see examples of appropriate Siemens scanner protocols, refer to:

http://www.nmr.mgh.harvard.edu/~andre/

For best results, each subject should have at least one sagittal structural scan. These scans are averaged and automatically corrected for motion before further processing.

The end result: FreeSurfer will produce a single, high quality 3D structural volume, corresponding 2D surfaces, and automatically segmented subcortical structures for each of your subjects. You can also use FreeSurfer to generate an average subject out of all the participants in your study, upon which you can display individual subject data -- structural and/or functional -- thus making FreeSurfer a practical option for individual and group analyses.

Work Flows

Consult the WorkFlows section to learn the detailed workings of a FreeSurfer processing stream.