FreeSurfer

FreeSurfer is an MRI brain imaging software package developed by the Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital with support from CorTechs Labs, Inc, La Jolla, CA. It is an important tool in functional brain mapping and facilitates the visualization of the functional regions of the highly-folded cerebral cortex. It contains both volume based and surface based analysis, which primarily use the white matter surface. FreeSurfer includes tools for the reconstruction of topologically correct and geometrically accurate models of both the gray/white and pial surfaces, for measuring cortical thickness, surface area and folding, and for computing inter-subject registration based on the pattern of cortical folds. In addition, an automated labeling of 35 non-cortical regions is included in the package.

Usage
The project's central process stream is called recon-all, which organizes raw MRI images into formats easily usable for morphometric and functional MRI statistical analysis with the FsFast package. Freesurfer uses a morphed spherical method to average across subjects for a GLM group analysis with the QDEC tool. Tkmedit and Tksurfer are the editing and visualization tools included in the package, but they will be replaced by Scuba when it is completed. The project also automatically segments the volume and parcellates the surface into standardized regions of interest (ROIs) that the Center for Morphometric Analysis has developed. The package has a broad spectrum of other uses, including retinotopy and cortical thickness analysis.

Interoperation
FreeSurfer interoperates easily with the FMRIB Software Library (FSL), which is a comprehensive library for image analysis, written by the Functional MRI of the Brain (FMRIB) group at Oxford, UK. The functional activation results obtained using either the FreeSurfer Functional Analysis Stream (FS-FAST) or the FSL tools can be overlayed onto inflated, sphered or flattened cortical surfaces using FreeSurfer. FreeSurfer also uses toolkits from MNI MINC, VXL, Tcl/Tk/Tix/BLT and Qt, which are all available with the distribution. Other neuroimaging programs like Caret and 3D Slicer can also import data processed by FreeSurfer.

Download
FreeSurfer runs on Mac OS and Linux. Free registration and installation are available. Documentation can be found on the FreeSurfer Wiki and free support is available from the developers and community through the FreeSurfer mailing list.