SPM SPM – introduction & orientation– introduction & orientation

introduction to the SPM softwareintroduction to the SPM softwareand resourcesand resources

Introduction to the SPM2 software…Introduction to the SPM2 software…

……a voxel by voxel hypothesis testing approacha voxel by voxel hypothesis testing approachTo make classical inferences about regionally specific To make classical inferences about regionally specific

effects while controlling type 1 erroreffects while controlling type 1 error

• Statistical Parametric MappingStatistical Parametric Mapping• General Linear ModelGeneral Linear Model• Random field theoryRandom field theory

What is SPM?What is SPM? 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 transformationsData transformations

RealignmentRealignment SmoothingSmoothing

NormalisationNormalisation

General linear modelGeneral linear model

Statistical parametric map (SPM)Statistical parametric map (SPM)Image time-seriesImage time-series

Parameter estimatesParameter estimates

Design matrixDesign matrix

TemplateTemplate

KernelKernel

Gaussian Gaussian field theoryfield theory

p <0.05p <0.05

StatisticalStatisticalinferenceinference

SPM GUI...SPM GUI...

• Spatial Spatial • realignment, spatial normalization, realignment, spatial normalization,

segmentation, coregistration, spatial segmentation, coregistration, spatial smoothingsmoothing

• StatisticalStatistical• voxel by voxel statistical analysisvoxel by voxel statistical analysis• general linear model, generalized for general linear model, generalized for

temporal autocorrelationtemporal autocorrelation• random effects analysesrandom effects analyses• multiple comparisons: Corrected multiple comparisons: Corrected pp--

values from random field theoryvalues from random field theory• plotting & results interrogationplotting & results interrogation

• UtilitiesUtilities• image display, CheckReg, rendering, image display, CheckReg, rendering,

brain extraction, adjusted means, brain extraction, adjusted means, image algebraimage algebra

• ImplementationImplementation• ““toolbox” of Mtoolbox” of MATLABATLAB®® functions functions• GUIGUI

• AvailabilityAvailability• open source academic freewareopen source academic freeware• documented and informally documented and informally

supportedsupported

SPM features…SPM features…

SPM resources…SPM resources…

SPM architectureSPM architecture• SPMSPM

– MatLab functions & scripts MatLab functions & scripts •• basic “toolbox” functions basic “toolbox” functions •• macro functions/scripts macro functions/scripts •• GUI functions & i/o primitives GUI functions & i/o primitives

– externally linked C-codeexternally linked C-code•• intensive operations intensive operations • • memory mappingmemory mapping

– platformplatform•• MatLab on UNIX, Linux, WindowsMatLab on UNIX, Linux, Windows

• MatLab:MatLab:– 4th Generation language4th Generation language

•• high level matrix based engineering maths language high level matrix based engineering maths language • • basic data type is matrix basic data type is matrix •• mathematical syntax mathematical syntax

– interpreted environmentinterpreted environment– graphics & GUI primitives providedgraphics & GUI primitives provided– programmingprogramming

•• scripts scripts •• functions (can compile) functions (can compile) • • objects objects • • linked C/C++linked C/C++

WorkstationWorkstation– developed on developed on Sun Solaris Sun Solaris UNIXUNIX– SolarisSolaris, , LinuxLinux & & WindowsWindows supported supported– other other UNIXUNIX– disk & memory…disk & memory…

Matlab 5.3.0 or laterMatlab 5.3.0 or later– no special “toolboxes” requiredno special “toolboxes” required

ANSIIANSII C Compiler C Compiler– to compile external C–mex routinesto compile external C–mex routines ready for ready for SolarisSolaris, , LinuxLinux, & , & WindowsWindows

Analyze / Analyze / MINCMINC format images format images– conversion programconversion program– extend SPMextend SPM

Internet accessInternet access……for for SPMwebSPMweb & the & the eemail discussion listmail discussion list

Plenty of timePlenty of time!!

SPM2 requirements…SPM2 requirements…

SPM Central

SPM documentation…SPM documentation…

peer reviewed literaturepeer reviewed literature SPM courseSPM course notes, notes,Human Brain Function &Human Brain Function &

SPM manualSPM manual

online help & online help & function descriptionsfunction descriptions

algorithm descriptions,algorithm descriptions,code annotations,code annotations,pseudo-codepseudo-code

• SPMSPMwebweb site sitehttp://www.fil.ion.ucl.ac.uk/spmhttp://www.fil.ion.ucl.ac.uk/spm

• SPM SPM eemail discussion listmail discussion listhttp://www.fil.ion.ucl.ac.uk/spm/helphttp://www.fil.ion.ucl.ac.uk/spm/help

spm@jiscmail.ac.ukspm@jiscmail.ac.uk

• MRC-CBU imagers MRC-CBU imagers (Matthew Brett)(Matthew Brett)http://www.mrc-cbu.cam.ac.uk/Imaging/http://www.mrc-cbu.cam.ac.uk/Imaging/

• Keith WorsleyKeith Worsleyhttp://www.math.mcgill.ca/~keith/http://www.math.mcgill.ca/~keith/

– FIL neuroscience resources linksFIL neuroscience resources linkshttp://www.fil.ion.ucl.ac.uk/Resources/http://www.fil.ion.ucl.ac.uk/Resources/

somesome SPM internet resources… SPM internet resources…

SPM Central

SPMwebSPMweb……

http://www.fil.ion.ucl.ac.uk/spmhttp://www.fil.ion.ucl.ac.uk/spm

• Introduction to SPM Introduction to SPM • The SPM distributionThe SPM distribution• SPM99SPM99• SPM2SPM2• Documentation & supportDocumentation & support• SPM SPM eemail discussion listmail discussion list• SPM short courseSPM short course• SPM course notesSPM course notes• SnPM99SnPM99• Example data setsExample data sets

SPM Central

SPM – SPM – eemail discussion listmail discussion list

• spm@jiscmail.ac.ukspm@jiscmail.ac.uk– Web home pageWeb home page

• http://www.fil.ion.ucl.ac.uk/spm/helphttp://www.fil.ion.ucl.ac.uk/spm/help• Archives, archive searches, membership lists, instructionsArchives, archive searches, membership lists, instructions

– SubscribeSubscribe• http://www.jiscmail.ac.uk/http://www.jiscmail.ac.uk/• eemail mail jiscmail@jiscmail.ac.ukjiscmail@jiscmail.ac.uk

– join spm join spm Firstname LastnameFirstname Lastname– Participate & learnParticipate & learn

• eemail mail spm@jiscmail.ac.ukspm@jiscmail.ac.uk• Monitored by SPMauthorsMonitored by SPMauthors• Usage queries, theoretical discussions, Usage queries, theoretical discussions,

bug reports, patches, techniques, &c…bug reports, patches, techniques, &c…

spm@jiscmail.ac.ukspm@jiscmail.ac.ukhttp://www.fil.ion.ucl.ac.uk/spm/helphttp://www.fil.ion.ucl.ac.uk/spm/help