Software Packages for Data Procesing

Freesurfer & FS Fast

Freesurfer is a set of automated and semi-automated tools for the segmentation, reconstruction, and processing of surface-models of the human cerebral cortex. These models have various uses and provide a powerful domain for the visualization of functional and structural neuroimaging data. With these tools, it is relatively easy to generate geometrically accurate and topologically correct models of the cerebral cortex. Calculations of morphometric quantities (e.g. cortical thickness, sulcal depth) are produced as part of the reconstruction procedure. In addition, FreeSurfer supports a novel inter-subject averaging procedure that is based on the alignment of cortical folding patterns in a spherical coordinate system. Facilitated by the spherical coordinate system, functional and structural properties of the cortex can be computed, analyzed and visualized in a single integrated set of tools. (See publications describing the techniques used in FreeSurfer.)

Integrated into the Freesurfer package is FS-FAST, the FreeSurfer Funtional Analysis STream. FS-FAST allows users to analyze their funtional MRI data, providing support for motion correction, spatial smoothing, intensity normalization, first-level GLM analysis, optimal experimental design, inter-subject registration and analysis, and visualization. It interfaces seamlessly to FreeSurfer allowing users to visualize their functional data on the inflated surface, perform high-resolution inter-subject registration using a surface-based atlas, and analyze their functional data using the cortical and subcortical regions-of-interest automatically generated by FreeSurfer.

FreeSurfer runs on Linux, Solaris, Mac OS/X and IRIX, and is relatively easy to install and run. The tools can be accessed through the graphical user interface, or from the command line.

For more information, visit the FREESURFER Homepage