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SPM – introduction & orientation
introduction to the SPM software
and resources
Introduction to the SPM2 software…
What is SPM?
…a voxel by voxel hypothesis testing approach
To make classical inferences about regionally specific
effects while controlling type 1 error
• Statistical Parametric Mapping
• General Linear Model
• Random field theory
“
Statistical Parametric Mapping
refers to the construction and
assessment of spatially
extended statistical process
used to test hypotheses about
[neuroimaging data from
SPECT/PET & fMRI.
These ideas have been
instantiated in software that is
called SPM.
”
Data transformations
Statistical parametric map (SPM)
Image time-series
Kernel
Design matrix
Realignment
Smoothing
General linear model
Statistical
inference
Normalisation
Gaussian
field theory
p <0.05
Template
Parameter estimates
SPM GUI...
SPM features…
• Spatial
• realignment, spatial normalization,
segmentation, coregistration, spatial
smoothing
• Statistical
• voxel by voxel statistical analysis
• general linear model, generalized for
temporal autocorrelation
• random effects analyses
• multiple comparisons: Corrected pvalues from random field theory
• plotting & results interrogation
• Utilities
• image display, CheckReg, rendering,
brain extraction, adjusted means,
image algebra
• Implementation
• “toolbox” of MATLAB® functions
• GUI
• Availability
• open source academic freeware
• documented and informally
supported
SPM resources…
SPM architecture
• SPM
– MatLab functions & scripts
• basic “toolbox” functions • macro functions/scripts
• GUI functions & i/o primitives
– externally linked C-code
• intensive operations • memory mapping
– platform
• MatLab on UNIX, Linux, Windows
• MatLab:
– 4th Generation language
• high level matrix based engineering maths language
• basic data type is matrix • mathematical syntax
– interpreted environment
– graphics & GUI primitives provided
– programming
• scripts • functions (can compile) • objects • linked C/C++
SPM2 requirements…
Workstation
–
–
–
–
developed on Sun Solaris UNIX
Solaris, Linux & Windows supported
other UNIX
disk & memory…
Matlab 5.3.0 or later
– no special “toolboxes” required
ANSII C Compiler
– to compile external C–mex routines
ready for Solaris, Linux, & Windows
Analyze / MINC format images
– conversion program
– extend SPM
Internet access
…for SPMweb & the email discussion list
SPM Central
Plenty of time!
SPM documentation…
peer reviewed literature
online help &
function descriptions
SPM course notes,
Human Brain Function &
SPM manual
algorithm descriptions,
code annotations,
pseudo-code
some
SPM internet resources…
• SPMweb site
SPM Central
http://www.fil.ion.ucl.ac.uk/spm
• SPM email discussion list
http://www.fil.ion.ucl.ac.uk/spm/help
[email protected]
• MRC-CBU imagers (Matthew Brett)
http://www.mrc-cbu.cam.ac.uk/Imaging/
• Keith Worsley
http://www.math.mcgill.ca/~keith/
– FIL neuroscience resources links
http://www.fil.ion.ucl.ac.uk/Resources/
SPMweb…
• Introduction to SPM
• The SPM distribution
• SPM99
• SPM2
• Documentation & support
• SPM email discussion list
• SPM short course
• SPM course notes
• SnPM99
• Example data sets
SPM Central
http://www.fil.ion.ucl.ac.uk/spm
SPM – email discussion list
• [email protected]
– Web home page
• http://www.fil.ion.ucl.ac.uk/spm/help
• Archives, archive searches, membership lists, instructions
– Subscribe
• http://www.jiscmail.ac.uk/
• email [email protected]
– join spm Firstname Lastname
– Participate & learn
• email [email protected]
• Monitored by SPMauthors
• Usage queries, theoretical discussions,
bug reports, patches, techniques, &c…
http://www.fil.ion.ucl.ac.uk/spm/help
[email protected]
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