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Installing the brain volume estimation SPM extension

System Requirements

spm_segment requires Matlab and the SPM package, which are available for most operating systems.


  • Ensure you have a working version of the required packages mentioned above
  • Download the software from here
  • Unzip spm_segment_<version>.zip
  • Open the file spm_segment_defaults.m in a text editor.
  • Edit the line beginning script_path= to point to the folder in which these scripts are located
  • This completes the setup of spm_segment where a command line interface is not required. See software usage for details on how to start spm_segment from a running SPM window
  • To configure the command line interface on Unix based systems (includes Linux, Mac OS X and Cygwin), make the following additional changes to spm_segment_defaults.m
    • Change the line version='SPM99' to your prefered default version.
    • Edit the line beginning matlab_path= to point to the directory containing the matlab executable
    • Edit the paths spm99_path= , spm2_path= and spm5_path= appropriately
  • For experts only, some segmentation parameters may be set in spm_segment_defaults.m

Visual assessment

Graphical tools to assess the accuracy of a segmentation are available on request.

Important information regarding the implementation

  • When using SPM5, the segmentation generated by spm_segment will differ slightly compared to segmentations processed through the SPM interface.
  • This is because there are two segmentation algorithms implemented in SPM5
    • The new algorithm, based on Ashburner, J. & Friston, K. J., Unified segmentation. Neuroimage, 2005, 26, 839-851
    • The old algorithm, based on Ashburner, J. & Friston, K. J., Voxel-based morphometry--the methods, Neuroimage, 2000, 11, 805-821
  • spm_segment calls the old algorithm
  • We are currently validating new algorithm and it will be available as an option in spm_segment shortly

Release Notes

  • 2008-04-01
  • - fixed a newline/carriage return bug which caused the command line scripts to fail with text files created in Microsoft Windows
    - default segmentation options are now set in spm_segment_defaults.m
    - fixed a bug causing the command line scripts to fail if absolute path names were given
  • 2008-03-26
  • - fixed an incompatibility which caused the GUI interface to fail in SPM5
  • 2007-10-25
  • - fixed a bug that caused the spm_segment command line interface to fail on Fedora Core 5
  • 2007-10-23
  • - added Matlab version option to command line interface
  • 2007-09-27
  • - fixed a bug that caused spm_segment to fail if a file existed with the same name as an image file, but without the '.img' extension
    - moved all system specific configuration and preferences to spm_segment_defaults.m
    - migrated web site from old template to current version, fixing display issues in some web browsers
  • 2006-01-06
  • - bug fix release
  • 2005-08-13
  • - beta version released

Segmented Brain Image

Last modified by Jon Jackson on Mon Dec 14 16:43:35 GMT 2009

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