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

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Presentation on theme: "SPM2 – introduction & orientation introduction to the SPM software some SPM resources introduction to the SPM software some SPM resources 2."— Presentation transcript:

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

2 Introduction to the SPM software…

3 Statistical Parametric MappingStatistical Parametric Mapping …a voxel by voxel hypothesis testing approach  reliably identify regions showing a significant experimental effect of interest TypeType I error – –significance test at each voxel –model voxel data, test parameters no exact prior anatomical hypothesisno exact prior anatomical hypothesis –multiple comparisons –General Linear Model –Random field theory SPMSPM …the software Statistical Parametric MappingStatistical Parametric Mapping …a voxel by voxel hypothesis testing approach  reliably identify regions showing a significant experimental effect of interest TypeType I error – –significance test at each voxel –model voxel data, test parameters no exact prior anatomical hypothesisno exact prior anatomical hypothesis –multiple comparisons –General Linear Model –Random field theory SPMSPM …the software What is SPM? the 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. “ ”

4 realignment & motion correction smoothing normalisation General Linear Model Ümodel fitting Üstatistic image corrected p-values image data parameter estimates design matrix anatomical reference kernel Statistical Parametric Map random field theory

5 SPM2 GUI…

6 SpatialSpatial realignment, spatial normalisation, segmentation, coregistration, spatial smoothingrealignment, spatial normalisation, segmentation, coregistration, spatial smoothing StatisticalStatistical voxel by voxel statistical analysisvoxel by voxel statistical analysis general linear model, generalised for temporal autocorrelationgeneral linear model, generalised for temporal autocorrelation ReML variance component estimationReML variance component estimation random effects analysesrandom effects analyses multiple comparisons: Corrected p-values from random field theorymultiple comparisons: Corrected p-values from random field theory Dynamic Causal ModellingDynamic Causal Modelling plotting & results interrogationplotting & results interrogation UtilitiesUtilities image display, CheckReg, rendering, image algebraimage display, CheckReg, rendering, image algebra SpatialSpatial realignment, spatial normalisation, segmentation, coregistration, spatial smoothingrealignment, spatial normalisation, segmentation, coregistration, spatial smoothing StatisticalStatistical voxel by voxel statistical analysisvoxel by voxel statistical analysis general linear model, generalised for temporal autocorrelationgeneral linear model, generalised for temporal autocorrelation ReML variance component estimationReML variance component estimation random effects analysesrandom effects analyses multiple comparisons: Corrected p-values from random field theorymultiple comparisons: Corrected p-values from random field theory Dynamic Causal ModellingDynamic Causal Modelling plotting & results interrogationplotting & results interrogation UtilitiesUtilities image display, CheckReg, rendering, image algebraimage display, CheckReg, rendering, image algebra SPM features…

7 SPM history… SPMclassic:SPMclassic: in-house MRC-CU –by KarlFriston & Jon Heather –by Karl Friston & Jon Heather released to the emerging functional neuroimaging community in 1991 why freely distribute?why freely distribute? –community –open –promote rigour (in emerging field) –promote collaboration –common analysis framework SPMclassic:SPMclassic: in-house MRC-CU –by KarlFriston & Jon Heather –by Karl Friston & Jon Heather released to the emerging functional neuroimaging community in 1991 why freely distribute?why freely distribute? –community –open –promote rigour (in emerging field) –promote collaboration –common analysis framework SPM94+ (SPM95, SPM96, SPM99,SPM2…)SPM94+ (SPM95, SPM96, SPM99,SPM2…) developed under auspices of the Wellcome Department of Cognitive Neurology –completely rewritten primary authors Karl Friston, John Ashburner, Andrew Holmes, Jean-Baptiste Poline, Philippe Ciuciu, Matthew Brett, Volkmar Glauche & Darren GitelmanKarl Friston, John Ashburner, Andrew Holmes, Jean-Baptiste Poline, Philippe Ciuciu, Matthew Brett, Volkmar Glauche & Darren Gitelman key collaborator Keith WorsleyKeith Worsley –GUI –support SPMweb, SPMhelp, SPMcourseSPMweb, SPMhelp, SPMcourse –SPM toolboxes (SnPM)(SnPM) MultivariateMultivariate DeformationsDeformations DICOMDICOM …

8 Constraints…Constraints… appropriate accessible available 2

9 SPM architecture SPMSPM –MatLab functions & scripts basic “toolbox” functions macro functions/scripts GUI functions & i/o primitives basic “toolbox” functions macro functions/scripts GUI functions & i/o primitives –externally linked C-code intensive operations memory mapping intensive operations memory mapping –platform MatLab on UNIX, Linux, Windows, MacOsX MatLab on UNIX, Linux, Windows, MacOsX MatLab:MatLab: –4th Generation language high level matrix based engineering maths language basic data type is matrix mathematical syntax 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++ scripts functions (can compile) objects linked C/C++ SPMSPM –MatLab functions & scripts basic “toolbox” functions macro functions/scripts GUI functions & i/o primitives basic “toolbox” functions macro functions/scripts GUI functions & i/o primitives –externally linked C-code intensive operations memory mapping intensive operations memory mapping –platform MatLab on UNIX, Linux, Windows, MacOsX MatLab on UNIX, Linux, Windows, MacOsX MatLab:MatLab: –4th Generation language high level matrix based engineering maths language basic data type is matrix mathematical syntax 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++ scripts functions (can compile) objects linked C/C++

10 SPM2 requirements… Workstation –developed on Sun Solaris UNIX –Solaris, Linux, MacOsX & Windows supported –other UNIX –disk & memory… Matlab or later –no special “toolboxes” required –SPM2 won’t work with Matlab 4 ANSII C Compiler –to compile external C–mex routines  ready for Solaris, Linux, MacOsX, & Windows Analyze / MINC / DICOM format images –conversion program –extend SPM Internet access …for SPMweb & the discussion list Plenty of time!

11 SPM resources…

12 SPM documentation… peer reviewed literature SPMcourse notes, Human Brain Function & SPM manual online help & function descriptions algorithm descriptions, code annotations, pseudo-code

13 Friston KJ (1997) “Imaging Cognitive Anatomy” Trends in Cognitive Sciences 1:21-27 Worsley KJ (1996) “The geometry of random images” CHANCE 9(1):27-40 Worsley KJ (1997) “An overview and some new developments in the statistical analysis of PET and fMRI data” Human Brain Mapping 5: Worsley KJ (1999) “Statistics of Brain Mapping” 52nd Session of the International Statistical Institute, Helsinki, Finland. Acton PD, Friston KJ (1998) “Statistical parametric mapping in functional neuroimaging: beyond PET and fMRI activation studies” European Journal of Nuclear Medicine 25: Rabe-Hesketh S, Bullmore ET, Brammer MJ (1997) “The analysis of functional magnetic resonance images” Statistical Methods in Medical Research 6(3): Petersson KM, Nichols TE, Poline J-B, Holmes AP (1999) “Statistical limitations in functional neuroimaging I: Non-inferential methods and statistical models” Phil. Trans. R. Soc. London. B 354: Petersson KM, Nichols TE, Poline J-B, Holmes AP (1999) “Statistical limitations in functional neuroimaging II: Signal detection and statistical inference” Phil. Trans. R. Soc. London. B 354: Friston KJ (1997) “Imaging Cognitive Anatomy” Trends in Cognitive Sciences 1:21-27 Worsley KJ (1996) “The geometry of random images” CHANCE 9(1):27-40 Worsley KJ (1997) “An overview and some new developments in the statistical analysis of PET and fMRI data” Human Brain Mapping 5: Worsley KJ (1999) “Statistics of Brain Mapping” 52nd Session of the International Statistical Institute, Helsinki, Finland. Acton PD, Friston KJ (1998) “Statistical parametric mapping in functional neuroimaging: beyond PET and fMRI activation studies” European Journal of Nuclear Medicine 25: Rabe-Hesketh S, Bullmore ET, Brammer MJ (1997) “The analysis of functional magnetic resonance images” Statistical Methods in Medical Research 6(3): Petersson KM, Nichols TE, Poline J-B, Holmes AP (1999) “Statistical limitations in functional neuroimaging I: Non-inferential methods and statistical models” Phil. Trans. R. Soc. London. B 354: Petersson KM, Nichols TE, Poline J-B, Holmes AP (1999) “Statistical limitations in functional neuroimaging II: Signal detection and statistical inference” Phil. Trans. R. Soc. London. B 354: Overview references…

14 SPMweb siteSPMweb sitehttp://www.fil.ion.ucl.ac.uk/spm SPM discussion listSPM discussion MRC-CBU imagers (Matthew Brett)MRC-CBU imagers (Matthew Brett)http://www.mrc-cbu.cam.ac.uk/Imaging/ Keith WorsleyKeith Worsleyhttp://www.math.mcgill.ca/~keith/ –FIL neuroscience resources links SPMweb siteSPMweb sitehttp://www.fil.ion.ucl.ac.uk/spm SPM discussion listSPM discussion MRC-CBU imagers (Matthew Brett)MRC-CBU imagers (Matthew Brett)http://www.mrc-cbu.cam.ac.uk/Imaging/ Keith WorsleyKeith Worsleyhttp://www.math.mcgill.ca/~keith/ –FIL neuroscience resources links some SPM internet resources…

15 SPMweb… Introduction to SPMIntroduction to SPM The SPM distributionThe SPM distribution SPM2SPM2 Documentation & supportDocumentation & support SPM discussion listSPM discussion list SPM short courseSPM short course SPM course notesSPM course notes SnPM’99SnPM’99 Example data setsExample data sets

16 SPM – discussion list –Web home page Archives, archive searches, membership lists, instructionsArchives, archive searches, membership lists, instructions –Subscribe –join spm Firstname Lastname –Parricipate & learn Monitored by SPMauthorsMonitored by SPMauthors Usage queries, theoretical discussions, bug reports, patches, techniques, &c…Usage queries, theoretical discussions, bug reports, patches, techniques, &c… –Web home page Archives, archive searches, membership lists, instructionsArchives, archive searches, membership lists, instructions –Subscribe –join spm Firstname Lastname –Parricipate & learn Monitored by SPMauthorsMonitored by SPMauthors Usage queries, theoretical discussions, bug reports, patches, techniques, &c…Usage queries, theoretical discussions, bug reports, patches, techniques, &c…


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