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FreeSurfer Beginners Guide

FreeSurfer is a freely available software package developed by investigators at the [http://www.nmr.mgh.harvard.edu: Athinoula A. Martinos Center for Biomedical Imaging] used for a number of procedures including:

Creation of computerized models of the brain from magnetic resonance imaging (MRI) data. [wiki:FsTutorial/MorphAndRecon link]
Processing of functional magnetic resonance imaging (fMRI) data. [wiki:FsFastTutorial link]
Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes [THICKNESS wiki link]
Intersubject averaging of structural and functional using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions [SPHERICAL wiki link]

Machine Requirements

To run Freesurfer, you will need either a PC running Linux or a Macintosh running OSX (OPTIMAL MACHINE wiki link).

Data Requirements

The processing procedures for the creation of cortical models requires good quality T1 weighted MRI data, such as a Siemens MPRAGE ([http://www.nmr.mgh.harvard.edu/~andre/: examples of appropriate Siemens scanner protocols])or GE SPGR sequence with approximately 1mm³ resolution (although a variety of quality datasets can be processed with additional manual intervention).

Getting Started

There is a variety of documentation about the use of Freesurfer contained in the Freesurfer wiki including [wiki:DownloadAndInstall installation of the software], [wiki:FsTutorial tutorials], [wiki:FsTutorial/Data sample data], and [wiki:WorkFlows work flows] providing step by step guides to performing specific tasks. To get started, we suggest you:
1. Install Freesurfer [wiki:DownloadAndInstall click here]
2. Download the sample dataset [wiki:FsTutorial/Data click here]
3. Follow the cortical reconstruction tutorial to create cortical models [wiki:FsTutorial click here]
4. Peruse the wiki to get a fuller knowledge of all of the available processing procedures in the Freesurfer software package

An active [wiki:FreeSurferSupport e-mail list] is available to answer specific questions about processing procedures.

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== Overview == An overview of the major processing steps taking place in a standard !FreeSurfer workflow are described in this PDF slide presentation: [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/FSL_anatomical_stream.pdf Building Anatomical Models with Freesurfer]. See also: FreeSurferAnalysisPipelineOverview The end result: FreeSurfer will produce a single, high quality 3D structural volume, corresponding 2D surfaces, and automatically segmented subcortical structures for each of your subjects. You can also use FreeSurfer to generate an average subject out of all the participants in your study, upon which you can display individual subject data -- structural and/or functional -- thus making FreeSurfer a practical option for individual and group analyses.