1. SPM Resources

2. SPM8 > Matlab 7.1 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++

3. SPM 8 BATCH

4. 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 ® functions“toolbox” 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 ® functions“toolbox” of MATLAB ® functions GUIGUI AvailabilityAvailability open source academic freewareopen source academic freeware documented and informally supporteddocumented and informally supported ToolboxesToolboxes

5. SPMweb… Introduction to SPMIntroduction to SPM SPM distribution: SPM2, SPM5, SPM8SPM distribution: SPM2, SPM5, SPM8 Documentation & BibliographyDocumentation & Bibliography SPM email discussion listSPM email discussion list SPM short courseSPM short course Example data setsExample data sets SPM extensionsSPM extensions http://www.fil.ion.ucl.ac.uk/spm/

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

7. 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 5:254-258 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 25:663-667 Rabe-Hesketh S, Bullmore ET, Brammer MJ (1997) “The analysis of functional magnetic resonance images” Statistical Methods in Medical Research 6(3):215-237 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 354:1239-1260 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 354:1239-1260 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 5:254-258 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 25:663-667 Rabe-Hesketh S, Bullmore ET, Brammer MJ (1997) “The analysis of functional magnetic resonance images” Statistical Methods in Medical Research 6(3):215-237 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 354:1239-1260 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 354:1239-1260 Overview references…

8. SPMOnlineBibliography

9. SPM – email discussion list spm@jiscmail.ac.ukspm@jiscmail.ac.uk –Web home page http://www.fil.ion.ucl.ac.uk/spm/support/http://www.fil.ion.ucl.ac.uk/spm/support/ Archives, archive searches, membership lists, instructionsArchives, archive searches, membership lists, instructions –Subscribe http://www.jiscmail.ac.uk/http://www.jiscmail.ac.uk/ email jiscmail@jiscmail.ac.ukemail jiscmail@jiscmail.ac.uk –join spm Firstname Lastname –Participate & learn email spm@jiscmail.ac.ukemail spm@jiscmail.ac.uk Monitored by SPMauthorsMonitored by SPMauthors Usage queries, theoretical discussions, bug reports, patches, techniques, &c…Usage queries, theoretical discussions, bug reports, patches, techniques, &c… spm@jiscmail.ac.ukspm@jiscmail.ac.uk –Web home page http://www.fil.ion.ucl.ac.uk/spm/support/http://www.fil.ion.ucl.ac.uk/spm/support/ Archives, archive searches, membership lists, instructionsArchives, archive searches, membership lists, instructions –Subscribe http://www.jiscmail.ac.uk/http://www.jiscmail.ac.uk/ email jiscmail@jiscmail.ac.ukemail jiscmail@jiscmail.ac.uk –join spm Firstname Lastname –Participate & learn email spm@jiscmail.ac.ukemail spm@jiscmail.ac.uk Monitored by SPMauthorsMonitored by SPMauthors Usage queries, theoretical discussions, bug reports, patches, techniques, &c…Usage queries, theoretical discussions, bug reports, patches, techniques, &c… spm@jiscmail.ac.uk http://www.fil.ion.ucl.ac.uk/spm/support/