FreeSurfer

FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging.

FreeSurfer provides many anatomical analysis tools, including: representation of the cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from the rest of the brain, skull stripping, B1 bias field correction, nonlinear registration of the cortical surface of an individual with a stereotaxic atlas, labeling of regions of the cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures and much more ...

• License: The license agreement that allows you to use FreeSurfer

• Release notes: New features and changes in each version of FreeSurfer - current stable release is v5.3.0

• Installation guide: How to download and install FreeSurfer on your computer

• Documentation: Getting started, step-by-step tutorials, FAQ, Glossary

• Citing FreeSurfer: Short description and citations for core FreeSurfer methods

• Publications: A Zotero library of articles on the methods in FreeSurfer and the studies that use FreeSurfer

• User support: How to get help with problems that you encounter when using FreeSurfer

• Hands-on training: Information on the FreeSurfer courses that we organize in Boston and around the world

• User contributions: Scripts and techniques from users of FreeSurfer.

• Acknowledgements: The funding agencies and collaborators that have contributed to the research behind FreeSurfer

• Social media: Find us on Facebook as FreeSurferMRI , follow us on Twitter or join our LinkedIn group .

Software

• 3D Slicer

• FSL

• AFNI/NIfTI/SUMA

• SPM - Statistical Parametric Mapping

• NITRC

• iSurf - iPhone/iPad app

• Nipype - Neuroimaging in Python, w/ FreeSurfer interfaces

• Mindboggle-101 data - Manually labeled anatomical regions for 101 healthy subjects

• MNE - M/EEG data analysis using FreeSurfer meshes and surface registration

• Brainstorm - See Integration with FreeSurfer

Documentation

Overview of FreeSurfer

• FreeSurferAnalysisPipelineOverview - Overview of the FreeSurfer analysis pipeline.

MRI Sequences

• Suggested Morphometry Sequences for Optimal FreeSurfer Reconstruction

• Alternative Morphometry Sequences, from ADNI

Troubleshooting

• Manual Editing: see Edits and LongitudinalEdits for an overview and check the Tutorials for examples.

• ReconAllTableStableV5.3 - An at-a-glance table showing the FreeSurfer files used & created during the recommended processing stream.

Some of Our Tools

• Registration Tools - Documentation of FreeSurfer's registration tools.

• LongitudinalProcessing - A description of the longitudinal stream in FreeSurfer.

• LongitudinalStatistics - Longitudinal linear mixed effects model MATLAB tools

• TRACULA - Documentation on TRActs Constrained by UnderLying Anatomy, a tool for automated probabilistic tractography.

More Details about FreeSurfer Processing

• WorkFlows - Information on how the FreeSurfer tools are used in a processing stream.

• ToolsAndCommands - GUI and command-line tool documentation.

• FileFormats - Description of native FreeSurfer file formats, as well as external file formats used by FreeSurfer.

• CoordinateSystems - Details on the voxel and RAS coordinate systems used in FreeSurfer.