FreeSurfer
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FreeSurfer is an MRI brain imaging software package developed by CorTechs Labs, Inc, La Jolla, CA and the Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital.
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[edit] Introduction
An important tool in functional brain mapping, FreeSurfer facilitates the visualization of the functional regions of the highly-folded cerebral cortex. It contains both volume based and surface based analysis, primarily using the white matter surface [1].
[edit] Download
FreeSurfer runs on Mac OS and Linux. Registration and installation are easy. Related documentation can be found on the FreeSurfer Wiki [2].
[edit] Usage
The project's central process stream is called recon-all [3], which organizes raw MRI images into formats easily usable for morphometric and functional MRI statistical analysis with the FsFast package. It uses a morphed spherical method to average across subjects. 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.
[edit] Interoperation
FreeSurfer is compatible 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 FSL tools can be overlayed onto inflated, sphered or flattened cortical surfaces using FreeSurfer.
[edit] 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
