SPM Software & Resources Wellcome Trust Centre for Neuroimaging University College London SPM Course London, October 2008.

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Presentation transcript:

SPM Software & Resources Wellcome Trust Centre for Neuroimaging University College London SPM Course London, October 2008

Normalisation Statistical Parametric Map Image time-series Parameter estimates General Linear Model RealignmentSmoothing Design matrix Anatomical reference Spatial filter Statistical Inference RFT p <0.05

Software: SPM8  Open Source academic freeware (under GPL)  Documented and informally supported  Requirements: –MATLAB: 7.1 (R14SP3) to 7.6 (R2008a) no toolboxes (EEG/MEG requires ‘signal’) –Supported platforms (MEX files): –Images File Format: Read: NIfTI-1 / Analyze Write: NIfTI-1 Import: DICOM, MINC, ECAT7 Linux (32 and 64 bit)Windows (32 and 64* bit) Mac Intel (32 bit) * soon

SPM8 installation  Download and install main distribution:  Download and install the updates: ftp://ftp.fil.ion.ucl.ac.uk/spm/spm8_updates/  Set MATLAB path: Add Folder (and not with Subfolders) Remove older SPM versions from the path

SPM Interface and Batch mode

SPM Toolboxes  User-contributed SPM extensions:

SPMweb  Introduction to SPM  SPM distribution: SPM2, SPM5, SPM8  Documentation & Bibliography  SPM discussion list  SPM short course  Example data sets  SPM extensions

External Resources  Wikipedia  Scholarpedia  WikiBooks  MRC-CBU Imaging wiki  NITRC

SPM Documentation Peer reviewed literature SPM Books: Human Brain Function I & II Statistical Parametric Mapping Online help & function descriptions SPM Manual

Overview references 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:

SPM Online Bibliography

SPM Mailing List   Web home page – –Archives, archive searches, instructions  Subscribe – – –join spm Firstname Lastname  Participate & learn – –Monitored by SPMauthors –Usage queries, theoretical discussions, bug reports, patches, techniques, &c…