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        To run Freesurfer, you will need either a PC running Linux or a Macintosh running OS X.           To run Freesurfer, you will need either a PC running Linux or a Macintosh running OS X.
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        Freesurfer consumes a lot of processor time, memory resources and disk space, so it is recommended to run Freesurfer on as powerful a machine as you have available. For example, at MGH we typically run Linux CentOS 4 on 2.5GHz dual processor AMD Opterons w/ 4 to 8GB of DDR SDRAM, and 250GB of disk space.          Freesurfer consumes a lot of processor time, memory resources and disk space, so it is recommended to run Freesurfer on as powerful a machine as you have available. For example, at MGH we typically run Linux CentOS 4 on 2.5GHz dual processor AMD Opterons w/ 4 to 8GB of DDR SDRAM, and 250GB of disk space.
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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).  The best scans will have excellent gray/white matter contrast. Example slices each various quality scans are found here:

 * attachment:excellent_scan.tif excellent GM/WM contrast
 * attachment:very_good_scan.tif very good GM/WM contrast
 * attachment:good_scan.tif good GM/WM contrast
 * attachment:poor_scan.tif poor GM/WM contrast
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[wiki:FreeSurferWiki top]

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:

  1. Creation of computerized models of the brain from magnetic resonance imaging (MRI) data. [wiki:FsTutorial/MorphAndRecon link]

  2. Processing of functional magnetic resonance imaging (fMRI) data. [wiki:FsFastTutorial link]

  3. Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes. [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl00-cortical-thickness.pdf link]

  4. Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions. [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99-morphing.pdf link]

Machine Requirements

  • To run Freesurfer, you will need either a PC running Linux or a Macintosh running OS X. Freesurfer consumes a lot of processor time, memory resources and disk space, so it is recommended to run Freesurfer on as powerful a machine as you have available. For example, at MGH we typically run Linux CentOS 4 on 2.5GHz dual processor AMD Opterons w/ 4 to 8GB of DDR SDRAM, and 250GB of disk space.

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). The best scans will have excellent gray/white matter contrast. Example slices each various quality scans are found here:

  • attachment:excellent_scan.tif excellent GM/WM contrast
  • attachment:very_good_scan.tif very good GM/WM contrast
  • attachment:good_scan.tif good GM/WM contrast
  • attachment:poor_scan.tif poor GM/WM contrast

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. Read the introductory material on Freesurfer from past lectures: [attachment:FSL_anatomical_stream.pdf slides (BF)] and [attachment:surferfest3.pdf slides (DG)]
    2. Read the background material: [wiki:ArticlesSlidesAndPosters click here]

    3. Install Freesurfer: [wiki:DownloadAndInstall click here]

    4. Download the sample dataset: [wiki:FsTutorial/Data click here]

    5. Follow the cortical reconstruction tutorial to create cortical models: [wiki:FsTutorial click here]

    6. 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.

FreeSurferBeginnersGuide (last edited 2020-04-10 10:31:15 by LeahMorgan)