SPM – introduction & orientation introduction to the SPM software and resources Data transformations Statistical parametric map (SPM) Image time-series Kernel Design matrix Realignment Smoothing General linear model Statistical inference Normalisation Gaussian field theory p <0.05 Template Parameter estimates 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, rendering, brain extraction, image algebra • Implementation • “toolbox” of MATLAB® functions • GUI • Availability • open source academic freeware • documented and informally supported SPM GUI... SPM resources… 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++ SPM5 requirements… Workstation – – – – developed on Sun Solaris UNIX Solaris, Linux, Mac & Windows supported other UNIX disk & memory… Matlab 6.5 - 7.1 – no special “toolboxes” required ANSII C Compiler – to compile external C–mex routines ready for Solaris, Linux, & Windows NIfTI/Analyze format images – conversion program – extend SPM Internet access …for SPMweb & the email discussion list S SP PM M C Ce en n tr tr al al Plenty of time! SPM documentation… peer reviewed literature online help & function descriptions SPM course notes, Human Brain Function & SPM manual algorithm descriptions, code annotations, pseudo-code & SPM5 Manual SPM Online Bibliography 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/ <[email protected]> • FIL neuroscience resources links http://www.fil.ion.ucl.ac.uk/resources.html • SPM Wiki http://en.wikibooks.org/wiki/SPM • MRC-CBU imagers http://www.mrc-cbu.cam.ac.uk/Imaging/Common/ S P M C e ntral S P M C e ntral 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/ SPM – email discussion list • [email protected] – 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 [email protected] – join spm Firstname Lastname – Participate & learn • email [email protected] • Monitored by SPMauthors • Usage queries, theoretical discussions, bug reports, patches, techniques, &c… http://www.fil.ion.ucl.ac.uk/spm/support/ [email protected]