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Developer(s)Martinos Center for Biomedical Imaging
Stable release
Operating systemLinux or Mac OS X
TypeNeuroimaging data analysis
LicenseFreeSurfer Software License[1]

FreeSurfer is a brain imaging software package developed by the Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital for analyzing magnetic resonance imaging (MRI) scan data. 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 tools to conduct both volume based and surface based analysis, which primarily use the white matter surface.[2] 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 FreeSurfer processing stream is controlled by a shell script called recon-all.[3] The script calls component programs that organize raw MRI images into formats easily usable for morphometric and functional MRI statistical analysis with the FreeSurfer Functional Analysis Stream (FS-FAST) package.[4] Freesurfer uses a morphed spherical method to average across subjects for statistical (general linear model) analysis with the QDEC[5] tool. Two editing and visualization tools, Tkmedit and Tksurfer, respectively, are included in the package, with an additional visualization tool called Freeview in development. FreeSurfer automatically segments the volume and parcellates the surface into standardized regions of interest (ROIs). The package has a broad spectrum of other uses, including retinotopy, brain morphometry, and other data analysis tools. Freesurfer can also do interhemispheric registration[6] and can also calculate the degree of folding or local GI.[7] Freesurfer also include a Matlab toolbox for linear mixed effects models[8]


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 overlaid onto inflated, sphered or flattened cortical surfaces using FreeSurfer. FreeSurfer also uses toolkits from MNI MINC, VXL, Tcl/Tk/Tix/BLT, VTK., KWWidgets and Qt,[9] which are all available with the distribution. Other neuroimaging programs like Caret, AFNI/SUMA, MNE, and 3D Slicer can also import data processed by FreeSurfer.


FreeSurfer runs on Mac OS and Linux. Free registration and binary installation are available without a cost, but a license key (text file) is necessary to run the FreeSurfer binaries.[10] Documentation can be found on the FreeSurfer Wiki[11] and limited support is available from the developers and community through the FreeSurfer mailing list.

See also


  1. ^ [1] FreeSurfer Software License page
  2. ^ Dale, Anders M.; Fischl, Bruce; Serenob, Martin I. (February 1999). "Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction" (PDF). NeuroImage. 9 (2): 179–194. doi:10.1006/nimg.1998.0395. PMID 9931268. Retrieved 29 August 2018.
  3. ^ [2] recon-all script usage
  4. ^ [3] FS-FAST Documentation
  5. ^ [4] QDEC Tutorial
  6. ^
  7. ^
  8. ^
  9. ^ [5] Developer's Guide
  10. ^ [6] Download notes
  11. ^ [7] FreeSurfer Wiki

External links