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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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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 1mm^3^ resolution (although a variety of quality datasets can be processed with additional manual intervention).	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 1mm^3^ resolution (although a variety of quality datasets can be processed with additional manual intervention).