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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 [1]. 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.



The project's central process stream is called recon-all,[2] 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.


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,[3] which are all available with the distribution. Other neuroimaging programs like Caret and 3D Slicer can also import data processed by FreeSurfer.


FreeSurfer runs on Mac OS and Linux. Free registration and installation are available. Documentation can be found on the FreeSurfer Wiki[4] and free support is available from the developers and community through the FreeSurfer mailing list.

See also

  • AFNI
  • Caret Van Essen Lab, Washington University in St. Louis
  • LONI Pipeline Laboratory of Neuro Imaging, UCLA
  • MNI MINC McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University
  • Statistical parametric mapping (SPM)
  • FMRIB Software Library
  • FreeSurfer Articles Overview and Contents Graham Wideman provides a comprehensive review of the FS pipeline with description of file formats.
  • Martinos Center detailed summary of FreeSurfer


  1. ^ [1] Dale, A. M., B. Fischl, et al. (1999). "Cortical surface-based analysis: Segmentation and surface reconstruction." Neuroimage 9(2): 179-94.
  2. ^ [2] Recommended Reconstruction Table
  3. ^ [3] Developer's Guide
  4. ^ [4] FreeSurfer Wiki
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "FreeSurfer". A list of authors is available in Wikipedia.
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