FreeSurfer Beginners Guide

FreeSurfer is a freely available software package developed by investigators at the 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.
  2. Processing of functional magnetic resonance imaging (fMRI) data.
  3. Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes.
  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.

Machine Requirements

Data Requirements

example_scan_A.jpg example_scan_B.jpg example_scan_C.jpg

Getting Started

where the input (-i) file is a single file representing a T1-weighted data set. If you have DICOM images, you must find a file in the T1 series to pass. You can do this with the dcmunack command.

An active e-mail list is available to answer specific questions about processing procedures.

There is also a FAQ

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