SPM2 – introduction & orientation introduction to the SPM software some SPM resources 2 Introduction to the SPM software… What is SPM? the game of the name • Statistical Parametric Mapping …a voxel by voxel hypothesis testing approach  reliably identify regions showing a significant experimental effect of interest • Type I error – significance test at each voxel – model voxel data, test parameters • no exact prior anatomical hypothesis – multiple comparisons – General Linear Model – Random field theory • SPM …the software “ Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical process used to test hypotheses about [neuro]imaging data from SPECT/PET & fMRI. These ideas have been instantiated in software that is called SPM. ” image data parameter estimates design matrix kernel realignment & motion correction General Linear Model smoothing model fitting statistic image random field theory normalisation anatomical reference Statistical Parametric Map corrected p-values SPM2 GUI… SPM features… • Spatial • realignment, spatial normalisation, segmentation, coregistration, spatial smoothing • Statistical • voxel by voxel statistical analysis • general linear model, generalised for temporal autocorrelation • ReML variance component estimation • random effects analyses • multiple comparisons: Corrected p-values from random field theory • Dynamic Causal Modelling • plotting & results interrogation • Utilities • image display, CheckReg, rendering, image algebra SPM history… • SPMclassic: in-house software @ MRC-CU – by Karl Friston & Jon Heather released to the emerging functional neuroimaging community in 1991 • why freely distribute? – – – – – community open promote rigour (in emerging field) promote collaboration common analysis framework • SPM94+ (SPM95, SPM96, SPM99,SPM2…) developed under auspices of the Wellcome Department of Cognitive Neurology – completely rewritten • • primary authors Karl Friston, John Ashburner, Andrew Holmes, Jean-Baptiste Poline, Philippe Ciuciu, Matthew Brett, Volkmar Glauche & Darren Gitelman key collaborator Keith Worsley – GUI – support • SPMweb, SPMhelp, SPMcourse – SPM toolboxes • • • • • (SnPM) Multivariate Deformations DICOM … 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, MacOsX • 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, MacOsX & Windows supported other UNIX disk & memory… Matlab 5.3.0 or later – no special “toolboxes” required – SPM2 won’t work with Matlab 4 ANSII C Compiler – to compile external C–mex routines ready for Solaris, Linux, MacOsX, & Windows Analyze / MINC / DICOM format images – conversion program – extend SPM Internet access …for SPMweb & the email discussion list SPM Central Plenty of time! SPM resources… SPM documentation… peer reviewed literature online help & function descriptions SPMcourse 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 • SPM2 • Documentation & support • SPM email discussion list • SPM short course • SPM course notes • SnPM’99 • 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 – Parricipate & 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