Mbirn: Freesurfer and tutorials

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Short Description
- FreeSurfer is a set of semi-automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface https://surfer.nmr.mgh.harvard.edu/
- Keywords: structural MRI, functional MRI, fMRI, morphometry,brain image processing, neuroscience

Longer Overview
- FreeSurfer is a set of software tools for the study of cortical and subcortical anatomy. In the cortical surface stream, the tools construct models of the boundary between white matter and cortical gray matter as well as the pial surface. Once these surfaces are known, an array of anatomical measures becomes possible, including: cortical thickness, surface area, curvature, and surface normal at each point on the cortex. The surfaces can be inflated and/or flattened for improved visualization. The surfaces can also be used to constrain the solutions to inverse optical, EEG and MEG problems. In addition, a cortical surfaced-based atlas has been defined based on average folding patterns mapped to a sphere. Surfaces from individuals can be aligned with this atlas with a high-dimensional nonlinear registration algorithm. The registration is based on aligning the cortical folding patterns and so directly aligns the anatomy instead of image intensities. The spherical atlas naturally forms a coordinate system in which point-to-point correspondence between subjects can be achieved. This coordinate system can then be used to create group maps (similar to how Talairach space is used for volumetric measurements). Most of the FreeSurfer pipeline is automated, which makes it ideal for use on large data sets.
- Freesurfer Analysis Pipeline Overview

Acknowledgements
- FreeSurfer is brought to you by CorTechs and the Athinoula A. Martinos Center for Biomedical Imaging (supported by NCRR/P41RR14075)

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