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SPM – introduction & orientation

SPM – introduction & orientation. introduction to the SPM software and resources. Statistical parametric map (SPM). Data transformations. Design matrix. Image time-series. Kernel. Realignment. Smoothing. General linear model. Gaussian field theory. Statistical inference.

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SPM – introduction & orientation

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

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

  3. Introduction to the SPM5 software…

  4. SPM features… • Spatial • realignment, spatial normalization, segmentation, coregistration, spatial smoothing • Statistical • voxel by voxel statistical analysis • general linear model, generalized for temporal autocorrelation • random effects analyses • multiple comparisons: Corrected p-values from random field theory • plotting & results interrogation • Utilities • image display, CheckReg, rendering, brain extraction, adjusted means, image algebra • Implementation • “toolbox” of MATLAB® functions • GUI • Availability • open source academic freeware • documented and informally supported

  5. SPM GUI...

  6. SPM resources…

  7. SPM architecture • SPM • MatLab functions & scripts • basic “toolbox” functions • macro functions/scripts • GUI functions & i/o primitives • externally linked C-code • intensive operations • memory mapping • platform • MatLab on UNIX, Linux, Windows • MatLab: • 4th Generation language • 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++

  8. SPM5b requirements… Workstation • developed on Sun Solaris UNIX • Solaris, Linux & Windows supported • other UNIX • disk & memory… Matlab 6.5 - 7.0 • no special “toolboxes” required ANSII C Compiler • to compile external C–mex routines • ready for Solaris, Linux, & Windows Analyze / MINC format images • conversion program • extend SPM Internet access …for SPMweb & the email discussion list Plenty of time!

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

  10. SPM Online Bibliography

  11. some SPM internet resources… • SPMweb site http://www.fil.ion.ucl.ac.uk/spm/ • SPM email discussion list http://www.fil.ion.ucl.ac.uk/spm/support/ <spm@jiscmail.ac.uk> • FIL neuroscience resources links http://www.fil.ion.ucl.ac.uk/resources.html • SPM Wikihttp://en.wikibooks.org/wiki/SPM • MRC-CBU imagers http://www.mrc-cbu.cam.ac.uk/Imaging/Common/

  12. SPMweb… • Introduction to SPM • SPM distribution:SPM99, SPM2, SPM5 • Documentation & Bibliography • SPM email discussion list • SPM short course • Example data sets • SPM extensions http://www.fil.ion.ucl.ac.uk/spm/

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

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