SPM 99 introduction orientation introduction to the SPM

SPM’ 99 – introduction & orientation introduction to the SPM software some SPM resources

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 Ümodel fitting Üstatistic image random field theory normalisation anatomical reference Statistical Parametric Map corrected p-values

SPM’ 99 GUI…

SPM features… • Spatial • realignment, spatial normalisation, segmentation, coregistration, spatial smoothing • Statistical • voxel by voxel statistical analysis • general linear model, generalised for temporal autocorrelation • random effects analyses • multiple comparisons: Corrected p-values from random field theory • plotting & results interrogation • Utilities • image display, Check. Reg, rendering, brain extraction, adjusted means, image algebra

SPM history… • SPMclassic: in-house software @ MRC-CU – by Karl Friston & Jon Heather released to the emerging functional neuroimaging community in 1991 • • SPM 94+ (SPM 95, SPM 96, SPM 99…) developed under auspices of the Wellcome Department of Cognitive Neurology – completely rewritten • why freely distribute? – – – community open promote rigour (in emerging field) promote collaboration common analysis framework • primary authors Karl Friston, John Ashburner, Andrew Holmes, Jean-Baptiste Poline key collaborator Keith Worsley – GUI – support • SPMweb, SPMhelp, SPMcourse – SPM toolboxes • • • Sn. PM Multivariate unwarp

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’ 99 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 – SPM’ 99 won’t work with Matlab 4 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 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’ 99 • SPM 2 – soon! • 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

SPM: Statistical Parametric Mapping Software for functional Neuro. Imaging 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 freely available software that is called SPM. Karl Friston John Ashburner Andrew Holmes Jean-Baptiste Poline Wellcome Department of Imaging Neuroscience

SPM short course 2002 hosted by The Wellcome Department of Imaging Neuroscience Institute of Neurology University College London

What is SPM? …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 • 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 [neuro]imaging data from SPECT/PET & f. MRI. These ideas have been instantiated in software that is called SPM. ”

image data smoothing kernel realignment & motion correction normalisation parameter estimates design matrix General Linear Model smoothing Ümodel fitting Üstatistic image random field theory SPM anatomical reference Statistical Parametric Map corrected p-values

image data parameter estimates design matrix kernel realignment & motion correction normalisation General Linear Model smoothing Ümodel fitting Üstatistic image random field theory SPM anatomical reference Statistical Parametric Map corrected p-values

SPM features… • Spatial • realignment, spatial normalisation, segmentation, coregistration, spatial smoothing • Statistical • voxel by voxel statistical analysis • general linear model, generalised for temporal autocorrelation • random effects analyses • multiple comparisons: Corrected p-values 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’ 99 GUI…