SPM – introduction & orientation introduction to the SPM software and resources Introduction to the SPM2 software… What is SPM? …a voxel by voxel hypothesis testing approach To make classical inferences about regionally specific effects while controlling type 1 error • Statistical Parametric Mapping • General Linear Model • Random field theory “ Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical process used to test hypotheses about [neuroimaging data from SPECT/PET & fMRI. These ideas have been instantiated in software that is called SPM. ” 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 GUI... 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 pvalues 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 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++ SPM2 requirements… Workstation – – – – developed on Sun Solaris UNIX Solaris, Linux & Windows supported other UNIX disk & memory… Matlab 5.3.0 or later – 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 SPM Central 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 some SPM internet resources… • SPMweb site SPM Central http://www.fil.ion.ucl.ac.uk/spm • SPM email discussion list http://www.fil.ion.ucl.ac.uk/spm/help spm@jiscmail.ac.uk • MRC-CBU imagers (Matthew Brett) http://www.mrc-cbu.cam.ac.uk/Imaging/ • Keith Worsley http://www.math.mcgill.ca/~keith/ – FIL neuroscience resources links http://www.fil.ion.ucl.ac.uk/Resources/ SPMweb… • Introduction to SPM • The SPM distribution • SPM99 • SPM2 • Documentation & support • SPM email discussion list • SPM short course • SPM course notes • SnPM99 • Example data sets SPM Central http://www.fil.ion.ucl.ac.uk/spm SPM – email discussion list • spm@jiscmail.ac.uk – Web home page • http://www.fil.ion.ucl.ac.uk/spm/help • 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/help spm@jiscmail.ac.uk