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SPM2 – introduction & orientation
introduction to the SPM software
some SPM resources
2
Introduction to the SPM software…
What is SPM?
the game of the name
• Statistical Parametric Mapping
…a voxel by voxel hypothesis testing approach
 reliably identify regions showing a
significant experimental effect of interest
• Type I error
– significance test at each voxel
– model voxel data, test parameters
• no exact prior anatomical hypothesis
– multiple comparisons
– General Linear Model
– Random field theory
• SPM
…the software
“
Statistical Parametric Mapping
refers to the construction and
assessment of spatially
extended statistical process
used to test hypotheses about
[neuro]imaging data from
SPECT/PET & fMRI.
These ideas have been
instantiated in software that is
called SPM.
”
image data
parameter
estimates
design
matrix
kernel
realignment &
motion
correction
General Linear Model
smoothing
model fitting
statistic image
random field theory
normalisation
anatomical
reference
Statistical
Parametric Map
corrected p-values
SPM2 GUI…
SPM features…
• Spatial
• realignment, spatial normalisation,
segmentation, coregistration, spatial
smoothing
• Statistical
• voxel by voxel statistical analysis
• general linear model, generalised for
temporal autocorrelation
• ReML variance component estimation
• random effects analyses
• multiple comparisons: Corrected p-values
from random field theory
• Dynamic Causal Modelling
• plotting & results interrogation
• Utilities
• image display, CheckReg, rendering, image
algebra
SPM history…
•
SPMclassic:
in-house software @ MRC-CU
– by Karl Friston & Jon Heather
released to the emerging functional
neuroimaging community in 1991
•
why freely distribute?
–
–
–
–
–
community
open
promote rigour (in emerging field)
promote collaboration
common analysis framework
•
SPM94+
(SPM95, SPM96, SPM99,SPM2…)
developed under auspices of the
Wellcome Department of Cognitive Neurology
– completely rewritten
•
•
primary authors
Karl Friston, John Ashburner, Andrew
Holmes, Jean-Baptiste Poline, Philippe
Ciuciu, Matthew Brett, Volkmar Glauche
& Darren Gitelman
key collaborator
Keith Worsley
– GUI
– support
• SPMweb, SPMhelp, SPMcourse
– SPM toolboxes
•
•
•
•
•
(SnPM)
Multivariate
Deformations
DICOM
…
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, MacOsX
• 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, MacOsX & Windows supported
other UNIX
disk & memory…
Matlab 5.3.0 or later
– no special “toolboxes” required
– SPM2 won’t work with Matlab 4
ANSII C Compiler
– to compile external C–mex routines
ready for Solaris, Linux, MacOsX, & Windows
Analyze / MINC / DICOM format images
– conversion program
– extend SPM
Internet access
…for SPMweb & the email discussion list
SPM Central
Plenty of time!
SPM resources…
SPM documentation…
peer reviewed literature
online help &
function descriptions
SPMcourse 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
• SPM2
• Documentation & support
• SPM email discussion list
• SPM short course
• SPM course notes
• SnPM’99
• 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
– Parricipate & 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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