SPM – introduction & orientation
introduction to the SPM software
and resources
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 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 p-values from
random field theory
• plotting & results interrogation
• Utilities
• image display, rendering, brain extraction, image
algebra
• Implementation
• “toolbox” of MATLAB® functions
• GUI
• Availability
• open source academic freeware
• documented and informally supported
SPM GUI...
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++
SPM5 requirements…
Workstation
–
–
–
–
developed on Sun Solaris UNIX
Solaris, Linux, Mac & Windows supported
other UNIX
disk & memory…
Matlab 6.5 - 7.1
– no special “toolboxes” required
ANSII C Compiler
– to compile external C–mex routines
ready for Solaris, Linux, & Windows
NIfTI/Analyze format images
– conversion program
– extend SPM
Internet access
…for SPMweb & the email discussion list
SPM
SPM Central
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
&
SPM5 Manual
SPM
Online
Bibliography
some
SPM internet resources…
• SPMweb site
http://www.fil.ion.ucl.ac.uk/spm/
• SPM email discussion list
http://www.fil.ion.ucl.ac.uk/spm/support/
<spm@jiscmail.ac.uk>
• FIL neuroscience resources links
http://www.fil.ion.ucl.ac.uk/resources.html
• SPM Wiki
http://en.wikibooks.org/wiki/SPM
• MRC-CBU imagers
http://www.mrc-cbu.cam.ac.uk/Imaging/Common/
SPM Central
SPM Central
SPMweb…
• Introduction to SPM
• SPM distribution:
SPM99, SPM2, SPM5
• Documentation &
Bibliography
• SPM email discussion
list
• SPM short course
• Example data sets
• SPM extensions
http://www.fil.ion.ucl.ac.uk/spm/
SPM – email discussion list
•
spm@jiscmail.ac.uk
– Web home page
• http://www.fil.ion.ucl.ac.uk/spm/support/
• Archives, archive searches, membership lists, instructions
– Subscribe
• http://www.jiscmail.ac.uk/
• email jiscmail@jiscmail.ac.uk
– join spm Firstname Lastname
– Participate & learn
• email spm@jiscmail.ac.uk
• Monitored by SPMauthors
• Usage queries, theoretical discussions,
bug reports, patches, techniques, &c…
http://www.fil.ion.ucl.ac.uk/spm/support/
spm@jiscmail.ac.uk