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SPM – introduction & orientation introduction to the SPM software and resources introduction to the SPM software and resources.

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

1 SPM – introduction & orientation introduction to the SPM software and resources introduction to the SPM software and resources

2 Data transformations RealignmentSmoothing Normalisation General linear model Statistical parametric map (SPM) Image time-series Parameter estimates Design matrix Template Kernel Gaussian field theory p <0.05 Statisticalinference

3 SpatialSpatial realignment, spatial normalization, segmentation, coregistration, spatial smoothingrealignment, spatial normalization, segmentation, coregistration, spatial smoothing StatisticalStatistical voxel by voxel statistical analysisvoxel by voxel statistical analysis general linear model, generalized for temporal autocorrelationgeneral linear model, generalized for temporal autocorrelation random effects analysesrandom effects analyses multiple comparisons: Corrected p-values from random field theorymultiple comparisons: Corrected p-values from random field theory plotting & results interrogationplotting & results interrogation UtilitiesUtilities image display, rendering, brain extraction, image algebraimage display, rendering, brain extraction, image algebra ImplementationImplementation toolbox of MATLAB ® functionstoolbox of MATLAB ® functions GUIGUI AvailabilityAvailability open source academic freewareopen source academic freeware documented and informally supporteddocumented and informally supported SpatialSpatial realignment, spatial normalization, segmentation, coregistration, spatial smoothingrealignment, spatial normalization, segmentation, coregistration, spatial smoothing StatisticalStatistical voxel by voxel statistical analysisvoxel by voxel statistical analysis general linear model, generalized for temporal autocorrelationgeneral linear model, generalized for temporal autocorrelation random effects analysesrandom effects analyses multiple comparisons: Corrected p-values from random field theorymultiple comparisons: Corrected p-values from random field theory plotting & results interrogationplotting & results interrogation UtilitiesUtilities image display, rendering, brain extraction, image algebraimage display, rendering, brain extraction, image algebra ImplementationImplementation toolbox of MATLAB ® functionstoolbox of MATLAB ® functions GUIGUI AvailabilityAvailability open source academic freewareopen source academic freeware documented and informally supporteddocumented and informally supported SPM features…

4 SPM GUI...

5 SPM resources…

6 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 MatLab on UNIX, Linux, Windows 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 MatLab on UNIX, Linux, Windows 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++

7 Workstation –developed on Sun Solaris UNIX –Solaris, Linux, Mac & Windows supported –other UNIX –disk & memory… Matlab –no special toolboxes required ANSII C Compiler –to compile external C–mex routines ready for Solaris, Linux, & Windows ready for Solaris, Linux, & Windows NIfTI/Analyze format images –conversion program –extend SPM Internet access …for SPMweb & the discussion list Plenty of time! SPM5 requirements…

8 SPM documentation… peer reviewed literature SPM course notes, Human Brain Function & SPM manual online help & function descriptions algorithm descriptions, code annotations, pseudo-code & SPM5 Manual

9 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…

10 SPMOnlineBibliography

11 some SPM internet resources… SPMweb siteSPMweb sitehttp://www.fil.ion.ucl.ac.uk/spm/ SPM discussion listSPM discussion FIL neuroscience resources linksFIL neuroscience resources linkshttp://www.fil.ion.ucl.ac.uk/resources.html SPM Wiki Wiki MRC-CBU imagersMRC-CBU imagershttp://www.mrc-cbu.cam.ac.uk/Imaging/Common/ SPMweb siteSPMweb sitehttp://www.fil.ion.ucl.ac.uk/spm/ SPM discussion listSPM discussion FIL neuroscience resources linksFIL neuroscience resources linkshttp://www.fil.ion.ucl.ac.uk/resources.html SPM Wiki Wiki MRC-CBU imagersMRC-CBU imagershttp://www.mrc-cbu.cam.ac.uk/Imaging/Common/

12 SPMweb… Introduction to SPMIntroduction to SPM SPM distribution: SPM99, SPM2, SPM5SPM distribution: SPM99, SPM2, SPM5 Documentation & BibliographyDocumentation & Bibliography SPM discussion listSPM discussion list SPM short courseSPM short course Example data setsExample data sets SPM extensionsSPM extensions

13 SPM – discussion list –Web home page Archives, archive searches, membership lists, instructionsArchives, archive searches, membership lists, instructions –Subscribe –join spm Firstname Lastname –Participate & 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 –Participate & 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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