SPM’99 SPM’99 – introduction & orientation – introduction & orientation introduction to the SPM software introduction to the SPM software some SPM resources some SPM resources
SPM’99 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources.
Dec 23, 2015
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SPM’99 SPM’99 – introduction & orientation– introduction & orientationSPM’99 SPM’99 – 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
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
SPM’99 GUI…SPM’99 GUI…SPM’99 GUI…SPM’99 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• random effects analysesrandom effects analyses• multiple comparisons: Corrected multiple comparisons: Corrected pp-values -values
from random field theoryfrom random field theory• plotting & results interrogationplotting & results interrogation
• UtilitiesUtilities• image display, CheckReg, rendering, brain image display, CheckReg, rendering, brain
extraction, adjusted means, image algebraextraction, adjusted means, image algebra
• 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• random effects analysesrandom effects analyses• multiple comparisons: Corrected multiple comparisons: Corrected pp-values -values
from random field theoryfrom random field theory• plotting & results interrogationplotting & results interrogation
• UtilitiesUtilities• image display, CheckReg, rendering, brain image display, CheckReg, rendering, brain
extraction, adjusted means, image algebraextraction, adjusted means, image algebra
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…)(SPM95, SPM96, SPM99…)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 PolineHolmes, Jean-Baptiste Poline
key collaboratorkey collaborator• Keith WorsleyKeith Worsley
– GUIGUI– supportsupport
• SPMweb, SPMhelp, SPMcourseSPMweb, SPMhelp, SPMcourse– SPM toolboxesSPM toolboxes
• SnPMSnPM• MultivariateMultivariate• unwarpunwarp
• SPM94+ SPM94+ (SPM95, SPM96, SPM99…)(SPM95, SPM96, SPM99…)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 PolineHolmes, Jean-Baptiste Poline
key collaboratorkey collaborator• Keith WorsleyKeith Worsley
– GUIGUI– supportsupport
• SPMweb, SPMhelp, SPMcourseSPMweb, SPMhelp, SPMcourse– SPM toolboxesSPM toolboxes
• SnPMSnPM• MultivariateMultivariate• unwarpunwarp
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, 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++
• 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– SPM’99 won’t work with Matlab 4SPM’99 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, & , & 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!!
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– SPM’99 won’t work with Matlab 4SPM’99 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, & , & 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!!
SPM’99 requirements…SPM’99 requirements…SPM’99 requirements…SPM’99 requirements…
SPM CentralSPM Central
SPM resources…SPM resources…SPM resources…SPM resources…
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
• 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
SPMwebSPMweb……SPMwebSPMweb……
http://www.fil.ion.ucl.ac.uk/spm
• Introduction to SPM Introduction to SPM
• The SPM distributionThe SPM distribution
• SPM’99SPM’99
• SPM2 SPM2 – – soon!soon!
• 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
• SPM’99SPM’99
• SPM2 SPM2 – – soon!soon!
• 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 setsSPM CentralSPM Central
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
Karl FristonJohn AshburnerAndrew Holmes
Jean-Baptiste Poline
Karl FristonJohn AshburnerAndrew Holmes
Jean-Baptiste Poline
SPM: Statistical Parametric MappingSPM: Statistical Parametric MappingSoftware for functional NeuroImagingSoftware for functional NeuroImaging
SPM: Statistical Parametric MappingSPM: Statistical Parametric MappingSoftware for functional NeuroImagingSoftware for functional NeuroImaging
Wellcome Department of Imaging NeuroscienceWellcome Department of Imaging NeuroscienceWellcome Department of Imaging NeuroscienceWellcome Department of Imaging Neuroscience
Statistical Parametric MappingStatistical Parametric Mapping refers to the construction and refers to the construction and assessment of spatially extended statistical process used to test assessment of spatially extended statistical process used to test
hypotheses about [neuro]imaging data from SPECT/PET & fMRI. hypotheses about [neuro]imaging data from SPECT/PET & fMRI. These ideas have been instantiated in freely available software These ideas have been instantiated in freely available software
that is called SPM.that is called SPM.
Statistical Parametric MappingStatistical Parametric Mapping refers to the construction and refers to the construction and assessment of spatially extended statistical process used to test assessment of spatially extended statistical process used to test
hypotheses about [neuro]imaging data from SPECT/PET & fMRI. hypotheses about [neuro]imaging data from SPECT/PET & fMRI. These ideas have been instantiated in freely available software These ideas have been instantiated in freely available software
that is called SPM.that is called SPM.
SPM short course 2002SPM short course 2002SPM short course 2002SPM short course 2002
hosted byhosted by
The Wellcome Department of Imaging NeuroscienceThe Wellcome Department of Imaging NeuroscienceInstitute of NeurologyInstitute of Neurology
University College LondonUniversity College London
……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
• Statistical Parametric MappingStatistical Parametric Mapping• General Linear ModelGeneral Linear Model
• Random field theoryRandom field theory
What is SPM?What is SPM?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 [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
parameterestimatesdesign
matrix
anatomicalreference
smoothingkernel
image data
StatisticalParametric Map
random field theory
SPMSPMSPMSPM
realignment &motion
correction
smoothing
normalisation
General Linear Modelmodel fittingstatistic image
corrected p-values
parameterestimatesdesign
matrix
anatomicalreference
kernel
image data
StatisticalParametric Map
random field theory
SPMSPMSPMSPM
SPM features…SPM features…SPM features…SPM features…
• 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• random effects analysesrandom effects analyses• multiple comparisons: Corrected multiple comparisons: Corrected pp-values -values
from random field theoryfrom random field theory• plotting & results interrogationplotting & results interrogation
• UtilitiesUtilities• image display, CheckReg, rendering, brain image display, CheckReg, rendering, brain
extraction, adjusted means, image algebraextraction, adjusted means, image algebra• ImplementationImplementation
• ““toolbox” of Mtoolbox” of MATLABATLAB®® functions functions• GUIGUI
• AvailabilityAvailability• open source academic freewareopen source academic freeware• documented and informally supporteddocumented and informally supported
• 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• random effects analysesrandom effects analyses• multiple comparisons: Corrected multiple comparisons: Corrected pp-values -values
from random field theoryfrom random field theory• plotting & results interrogationplotting & results interrogation
• UtilitiesUtilities• image display, CheckReg, rendering, brain image display, CheckReg, rendering, brain
extraction, adjusted means, image algebraextraction, adjusted means, image algebra• ImplementationImplementation
• ““toolbox” of Mtoolbox” of MATLABATLAB®® functions functions• GUIGUI
• AvailabilityAvailability• open source academic freewareopen source academic freeware• documented and informally supporteddocumented and informally supported
SPM’99 GUI…SPM’99 GUI…SPM’99 GUI…SPM’99 GUI…
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