SPM introduction orientation introduction to the SPM software and resources introduction to the...
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SPM SPM – introduction & orientation– introduction & orientation
introduction to the SPM softwareintroduction to the SPM softwareand resourcesand resources
Introduction to the SPM2 software…Introduction to the SPM2 software…
……a voxel by voxel hypothesis testing approacha voxel by voxel hypothesis testing approachTo make classical inferences about regionally specific To make classical inferences about regionally specific
effects while controlling type 1 erroreffects while controlling type 1 error
• Statistical Parametric MappingStatistical Parametric Mapping• General Linear ModelGeneral Linear Model• Random field theoryRandom field theory
What is SPM?What is SPM? 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 transformationsData transformations
RealignmentRealignment SmoothingSmoothing
NormalisationNormalisation
General linear modelGeneral linear model
Statistical parametric map (SPM)Statistical parametric map (SPM)Image time-seriesImage time-series
Parameter estimatesParameter estimates
Design matrixDesign matrix
TemplateTemplate
KernelKernel
Gaussian Gaussian field theoryfield theory
p <0.05p <0.05
StatisticalStatisticalinferenceinference
SPM GUI...SPM GUI...
• Spatial Spatial • realignment, spatial normalization, realignment, spatial normalization,
segmentation, coregistration, spatial segmentation, coregistration, spatial smoothingsmoothing
• StatisticalStatistical• voxel by voxel statistical analysisvoxel by voxel statistical analysis• general linear model, generalized for general linear model, generalized for
temporal autocorrelationtemporal autocorrelation• random effects analysesrandom effects analyses• multiple comparisons: Corrected multiple comparisons: Corrected pp--
values from random field theoryvalues from random field theory• plotting & results interrogationplotting & results interrogation
• UtilitiesUtilities• image display, CheckReg, rendering, image display, CheckReg, rendering,
brain extraction, adjusted means, brain extraction, adjusted means, image algebraimage algebra
• ImplementationImplementation• ““toolbox” of Mtoolbox” of MATLABATLAB®® functions functions• GUIGUI
• AvailabilityAvailability• open source academic freewareopen source academic freeware• documented and informally documented and informally
supportedsupported
SPM features…SPM features…
SPM resources…SPM resources…
SPM architectureSPM architecture• SPMSPM
– MatLab functions & scripts MatLab functions & scripts •• basic “toolbox” functions basic “toolbox” functions •• macro functions/scripts macro functions/scripts •• GUI functions & i/o primitives GUI functions & i/o primitives
– externally linked C-codeexternally linked C-code•• intensive operations intensive operations • • memory mappingmemory mapping
– platformplatform•• MatLab on UNIX, Linux, WindowsMatLab on UNIX, Linux, Windows
• MatLab:MatLab:– 4th Generation language4th Generation language
•• high level matrix based engineering maths language high level matrix based engineering maths language • • basic data type is matrix basic data type is matrix •• mathematical syntax mathematical syntax
– interpreted environmentinterpreted environment– graphics & GUI primitives providedgraphics & GUI primitives provided– programmingprogramming
•• scripts scripts •• functions (can compile) functions (can compile) • • objects objects • • linked C/C++linked C/C++
WorkstationWorkstation– developed on developed on Sun Solaris Sun Solaris UNIXUNIX– SolarisSolaris, , LinuxLinux & & WindowsWindows supported supported– other other UNIXUNIX– disk & memory…disk & memory…
Matlab 5.3.0 or laterMatlab 5.3.0 or later– no special “toolboxes” requiredno special “toolboxes” required
ANSIIANSII C Compiler C Compiler– to compile external C–mex routinesto compile external C–mex routines ready for ready for SolarisSolaris, , LinuxLinux, & , & WindowsWindows
Analyze / Analyze / MINCMINC format images format images– conversion programconversion program– extend SPMextend SPM
Internet accessInternet access……for for SPMwebSPMweb & the & the eemail discussion listmail discussion list
Plenty of timePlenty of time!!
SPM2 requirements…SPM2 requirements…
SPM Central
SPM documentation…SPM documentation…
peer reviewed literaturepeer reviewed literature SPM courseSPM course notes, notes,Human Brain Function &Human Brain Function &
SPM manualSPM manual
online help & online help & function descriptionsfunction descriptions
algorithm descriptions,algorithm descriptions,code annotations,code annotations,pseudo-codepseudo-code
• SPMSPMwebweb site sitehttp://www.fil.ion.ucl.ac.uk/spmhttp://www.fil.ion.ucl.ac.uk/spm
• SPM SPM eemail discussion listmail discussion listhttp://www.fil.ion.ucl.ac.uk/spm/helphttp://www.fil.ion.ucl.ac.uk/spm/help
[email protected]@jiscmail.ac.uk
• MRC-CBU imagers MRC-CBU imagers (Matthew Brett)(Matthew Brett)http://www.mrc-cbu.cam.ac.uk/Imaging/http://www.mrc-cbu.cam.ac.uk/Imaging/
• Keith WorsleyKeith Worsleyhttp://www.math.mcgill.ca/~keith/http://www.math.mcgill.ca/~keith/
– FIL neuroscience resources linksFIL neuroscience resources linkshttp://www.fil.ion.ucl.ac.uk/Resources/http://www.fil.ion.ucl.ac.uk/Resources/
somesome SPM internet resources… SPM internet resources…
SPM Central
SPMwebSPMweb……
http://www.fil.ion.ucl.ac.uk/spmhttp://www.fil.ion.ucl.ac.uk/spm
• Introduction to SPM Introduction to SPM • The SPM distributionThe SPM distribution• SPM99SPM99• SPM2SPM2• Documentation & supportDocumentation & support• SPM SPM eemail discussion listmail discussion list• SPM short courseSPM short course• SPM course notesSPM course notes• SnPM99SnPM99• Example data setsExample data sets
SPM Central
SPM – SPM – eemail discussion listmail discussion list
• [email protected]@jiscmail.ac.uk– Web home pageWeb home page
• http://www.fil.ion.ucl.ac.uk/spm/helphttp://www.fil.ion.ucl.ac.uk/spm/help• Archives, archive searches, membership lists, instructionsArchives, archive searches, membership lists, instructions
– SubscribeSubscribe• http://www.jiscmail.ac.uk/http://www.jiscmail.ac.uk/• eemail mail [email protected]@jiscmail.ac.uk
– join spm join spm Firstname LastnameFirstname Lastname– Participate & learnParticipate & learn
• eemail mail [email protected]@jiscmail.ac.uk• Monitored by SPMauthorsMonitored by SPMauthors• Usage queries, theoretical discussions, Usage queries, theoretical discussions,
bug reports, patches, techniques, &c…bug reports, patches, techniques, &c…
[email protected]@jiscmail.ac.ukhttp://www.fil.ion.ucl.ac.uk/spm/helphttp://www.fil.ion.ucl.ac.uk/spm/help