SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2.

SPM2 SPM2 – introduction & orientation– introduction & orientationSPM2 SPM2 – introduction & orientation– introduction & orientation

introduction to the SPM softwareintroduction to the SPM software

some SPM resourcessome SPM resources

Introduction to the SPM software…Introduction to the SPM software…Introduction to the SPM software…Introduction to the SPM software…

• Statistical Parametric MappingStatistical Parametric Mapping……a voxel by voxel hypothesis testing approacha voxel by voxel hypothesis testing approach

reliably identify regions showing a reliably identify regions showing a significant experimental effect of interestsignificant experimental effect of interest

• TypeType I error– significance test at each voxel– model voxel data, test parametersmodel voxel data, test parameters

• no exact prior anatomical hypothesisno exact prior anatomical hypothesis– multiple comparisonsmultiple comparisons

– General Linear ModelGeneral Linear Model– Random field theoryRandom field theory

• SPMSPM……the softwarethe software

What is SPM?What is SPM?the game of the namethe game of the name

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.

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.

realignment &motion

correction

smoothing

normalisation

General Linear Modelmodel fittingstatistic image

corrected p-values

image data parameterestimatesdesign

matrix

anatomicalreference

kernel

StatisticalParametric Map

random field theory

SPM2 GUI…SPM2 GUI…SPM2 GUI…SPM2 GUI…

• Spatial Spatial • realignment, spatial normalisation, realignment, spatial normalisation,

segmentation, coregistration, spatial segmentation, coregistration, spatial smoothingsmoothing

• StatisticalStatistical• voxel by voxel statistical analysisvoxel by voxel statistical analysis• general linear model, generalised for general linear model, generalised for

temporal autocorrelationtemporal autocorrelation• ReML variance component estimationReML variance component estimation• random effects analysesrandom effects analyses• multiple comparisons: Corrected multiple comparisons: Corrected pp-values -values

from random field theoryfrom random field theory• Dynamic Causal ModellingDynamic Causal Modelling• plotting & results interrogationplotting & results interrogation

• UtilitiesUtilities• image display, CheckReg, rendering, image image display, CheckReg, rendering, image

algebraalgebra

• Spatial Spatial • realignment, spatial normalisation, realignment, spatial normalisation,

segmentation, coregistration, spatial segmentation, coregistration, spatial smoothingsmoothing

• StatisticalStatistical• voxel by voxel statistical analysisvoxel by voxel statistical analysis• general linear model, generalised for general linear model, generalised for

temporal autocorrelationtemporal autocorrelation• ReML variance component estimationReML variance component estimation• random effects analysesrandom effects analyses• multiple comparisons: Corrected multiple comparisons: Corrected pp-values -values

from random field theoryfrom random field theory• Dynamic Causal ModellingDynamic Causal Modelling• plotting & results interrogationplotting & results interrogation

• UtilitiesUtilities• image display, CheckReg, rendering, image image display, CheckReg, rendering, image

algebraalgebra

SPM features…SPM features…SPM features…SPM features…

SPM history…SPM history…SPM history…SPM history…

• SPMSPMclassicclassic::in-house software @ MRC-CUin-house software @ MRC-CU– by Karlby Karl Friston & Jon HeatherFriston & Jon Heather

released to the emerging functional released to the emerging functional neuroimaging community in 1991neuroimaging community in 1991

• why freely distribute?why freely distribute?– communitycommunity– openopen– promote rigour promote rigour (in emerging field)(in emerging field)

– promote collaborationpromote collaboration– common analysis frameworkcommon analysis framework

• SPMSPMclassicclassic::in-house software @ MRC-CUin-house software @ MRC-CU– by Karlby Karl Friston & Jon HeatherFriston & Jon Heather

released to the emerging functional released to the emerging functional neuroimaging community in 1991neuroimaging community in 1991

• why freely distribute?why freely distribute?– communitycommunity– openopen– promote rigour promote rigour (in emerging field)(in emerging field)

– promote collaborationpromote collaboration– common analysis frameworkcommon analysis framework

• SPM94+ SPM94+ (SPM95, SPM96, SPM99,SPM2…)(SPM95, SPM96, SPM99,SPM2…)

developed under auspices of the developed under auspices of the Wellcome Department of Cognitive NeurologyWellcome Department of Cognitive Neurology

– completely rewrittencompletely rewrittenprimary authorsprimary authors

• Karl Friston, John Ashburner, Andrew Karl Friston, John Ashburner, Andrew Holmes, Jean-Baptiste Poline, Philippe Holmes, Jean-Baptiste Poline, Philippe Ciuciu, Matthew Brett, Volkmar Glauche Ciuciu, Matthew Brett, Volkmar Glauche & Darren Gitelman& Darren Gitelman

key collaboratorkey collaborator• Keith WorsleyKeith Worsley

– GUIGUI– supportsupport

• SPMweb, SPMhelp, SPMcourseSPMweb, SPMhelp, SPMcourse– SPM toolboxesSPM toolboxes

• (SnPM)(SnPM)• MultivariateMultivariate• DeformationsDeformations• DICOMDICOM• ……

• SPM94+ SPM94+ (SPM95, SPM96, SPM99,SPM2…)(SPM95, SPM96, SPM99,SPM2…)

developed under auspices of the developed under auspices of the Wellcome Department of Cognitive NeurologyWellcome Department of Cognitive Neurology

– completely rewrittencompletely rewrittenprimary authorsprimary authors

• Karl Friston, John Ashburner, Andrew Karl Friston, John Ashburner, Andrew Holmes, Jean-Baptiste Poline, Philippe Holmes, Jean-Baptiste Poline, Philippe Ciuciu, Matthew Brett, Volkmar Glauche Ciuciu, Matthew Brett, Volkmar Glauche & Darren Gitelman& Darren Gitelman

key collaboratorkey collaborator• Keith WorsleyKeith Worsley

– GUIGUI– supportsupport

• SPMweb, SPMhelp, SPMcourseSPMweb, SPMhelp, SPMcourse– SPM toolboxesSPM toolboxes

• (SnPM)(SnPM)• MultivariateMultivariate• DeformationsDeformations• DICOMDICOM• ……

SPM architectureSPM architectureSPM 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, Windows, MacOsXMatLab on UNIX, Linux, Windows, MacOsX

• 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++