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

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

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Page 1: 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

2

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

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

Page 3: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

• 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

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.

Page 4: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

realignment &motion

correction

smoothing

normalisation

General Linear Modelmodel fittingstatistic image

corrected p-values

image data parameterestimatesdesign

matrix

anatomicalreference

kernel

StatisticalParametric Map

random field theory

Page 5: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

SPM2 GUI…SPM2 GUI…SPM2 GUI…SPM2 GUI…

Page 6: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

• 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…

Page 7: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

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• ……

Page 8: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

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++

• 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++

Page 9: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

SPM2 requirements…SPM2 requirements…SPM2 requirements…SPM2 requirements…

WorkstationWorkstation– developed on developed on Sun Solaris Sun Solaris UNIXUNIX– SolarisSolaris, , Linux, MacOsXLinux, MacOsX & & 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– SPM2 won’t work with Matlab 4SPM2 won’t work with Matlab 4

ANSIIANSII C Compiler C Compiler– to compile external C–mex routinesto compile external C–mex routines ready for ready for SolarisSolaris, , LinuxLinux, , MacOsXMacOsX, & , & WindowsWindows

Analyze / Analyze / MINCMINC / DICOM format images / DICOM 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!!

WorkstationWorkstation– developed on developed on Sun Solaris Sun Solaris UNIXUNIX– SolarisSolaris, , Linux, MacOsXLinux, MacOsX & & 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– SPM2 won’t work with Matlab 4SPM2 won’t work with Matlab 4

ANSIIANSII C Compiler C Compiler– to compile external C–mex routinesto compile external C–mex routines ready for ready for SolarisSolaris, , LinuxLinux, , MacOsXMacOsX, & , & WindowsWindows

Analyze / Analyze / MINCMINC / DICOM format images / DICOM 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!!SPM CentralSPM Central

Page 10: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

SPM resources…SPM resources…SPM resources…SPM resources…

Page 11: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

SPM documentation…SPM documentation…SPM documentation…SPM documentation…

peer reviewed literaturepeer reviewed literature SPMcourseSPMcourse 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

Page 12: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

• 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…somesome SPM internet resources… SPM internet resources…

SPM CentralSPM Central

Page 13: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

SPMwebSPMweb……SPMwebSPMweb……

• Introduction to SPM Introduction to SPM • The SPM distributionThe SPM distribution• SPM2SPM2• Documentation & supportDocumentation & support• SPM SPM eemail discussion listmail discussion list• SPM short courseSPM short course• SPM course notesSPM course notes• SnPM’99SnPM’99• Example data setsExample data sets

• Introduction to SPM Introduction to SPM • The SPM distributionThe SPM distribution• SPM2SPM2• Documentation & supportDocumentation & support• SPM SPM eemail discussion listmail discussion list• SPM short courseSPM short course• SPM course notesSPM course notes• SnPM’99SnPM’99• Example data setsExample data sets

http://www.fil.ion.ucl.ac.uk/spm

SPM CentralSPM Central

Page 14: SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2

SPM – SPM – eemail discussion listmail discussion listSPM – 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

– Parricipate & learnParricipate & 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.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

– Parricipate & learnParricipate & 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]://www.fil.ion.ucl.ac.uk/spm/help