SPM99 Manual - May 2001

Written by Dick Veltman and Chloe Hutton, with the help of John Ashburner, Rik Henson and other members of the FIL and ICN.


This document (PDF version) provides step-by-step guidelines for those who are not yet familiar with the use of SPM'99.

SPM has an extensive web site at:


Practical information regarding the downloading and installation of SPM can be found at:


Academic peer-reviewed papers providing a theoretical reference for SPM are available at:


Information about SPM courses and course notes can be accessed from:


Example data sets (which are also used in this manual) are available for downloading from:


Help is available via the Help option of the SPM interface, and more detailed help in using SPM is available through the SPM email list:


Third party documentation is also available. An extensive site describing many aspects of neuroimaging, including the use of SPM and links to image display software [Matthew Brett] can be found at:


Protocols and tools for use with SPM99 [Kalina Christoff] can be found at:

http://www-psych.stanford.edu/~kalina/SPM99 /.

Some useful snippets of code from the SPM email list for manipulation of images and results display [Tom Nichols] can be found at:


MRIcro - SPM compatible, Windows based software package for viewing medical images, converting image formats and identifying regions of interest [Chris Rorden] can be freely downloaded from:


Apologies if there are other useful sites that are not included here. Please remind us about them via the SPM email list.


The present version of SPM requires core MATLAB (version 5.2 or higher; Maths Works, Inc., Natick, MA, USA) to run. The image format used is the simple header and image file format of ANALYZE (Biomedical Imaging Resource, Mayo Foundation). In SPM, image headers can be edited (and created) using the HDR edit option (described in section 5 below). Several researchers have developed routines for conversion of other image formats to ANALYZE format, (e.g. MRIcro). Other information about image converters is also available via the email list.


  1. Getting started

  2. Spatial pre-processing

  3. Model specification and parameter estimation

  4. Results assessment

  5. Miscellaneous functions and Utilities