SPM introduction orientation introduction to the SPM software

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

Introduction to the SPM 2 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 & f. MRI. These ideas have been instantiated in software that is called SPM. ”

Data transformations Image time-series Kernel Design matrix Realignment Smoothing General linear model Statistical parametric map (SPM) 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, Check. Reg, 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 – 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 • 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 & 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 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 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 99 • 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 – 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