SPM 2 introduction orientation introduction to

SPM 2 – 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 & f. MRI. 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 Ü model fitting Ü statistic image random field theory normalisation anatomical reference Statistical Parametric Map corrected p-values

SPM 2 GUI…

SPM features… • Spatial • realignment, spatial normalisation, segmentation, coregistration, spatial smoothing • Statistical • voxel by voxel statistical analysis • general linear model, generalised for temporal autocorrelation • Re. ML variance component estimation • random effects analyses • multiple comparisons: Corrected p-values from random field theory • Dynamic Causal Modelling • plotting & results interrogation • Utilities • image display, Check. Reg, 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 • SPM 94+ (SPM 95, SPM 96, SPM 99, SPM 2…) developed under auspices of the Wellcome Department of Cognitive Neurology – completely rewritten • • primary authors Karl Friston, John Ashburner, Andrew Friston, Ashburner, Holmes, Jean-Baptiste Poline, Philippe Baptiste Poline, Jean. Ciuciu, Matthew Brett, Volkmar Glauche Ciuciu, & Darren Gitelman key collaborator Keith Worsley – GUI – support • SPMweb, SPMhelp, SPMcourse – SPM toolboxes • • • (Sn. PM) Multivariate Deformations DICOM …

SPM architecture • SPM – Mat. Lab functions & scripts • basic “toolbox” functions • macro functions/scripts • GUI functions & i/o primitives – externally linked C-code • intensive operations • memory mapping – platform • Mat. Lab on UNIX, Linux, Windows, Mac. Os. X • Mat. Lab: – 4 th 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++

SPM 2 requirements… Workstation – – developed on Sun Solaris UNIX Solaris, Linux, Mac. Os. X & Windows supported other UNIX disk & memory… Matlab 5. 3. 0 or later – no special “toolboxes” required – SPM 2 won’t work with Matlab 4 ANSII C Compiler – to compile external C–mex routines ®ready for Solaris, Linux, Mac. Os. X, & Windows Analyze / MINC / DICOM format images – conversion program – extend SPM Internet access …for SPMweb & the email discussion list 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 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 • SPM 2 • Documentation & support • SPM email discussion list • SPM short course • SPM course notes • Sn. PM’ 99 • Example data sets 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