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

SPM – introduction & orientationSPM – introduction & orientationSPM – introduction & orientationSPM – introduction & orientation

introduction to the SPM softwareintroduction to the SPM software

and resourcesand resources

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

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

coregistration, spatial smoothingcoregistration, spatial smoothing• StatisticalStatistical

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

autocorrelationautocorrelation• random effects analysesrandom effects analyses• multiple comparisons: Corrected multiple comparisons: Corrected pp-values from -values from

random field theoryrandom field theory• plotting & results interrogationplotting & results interrogation

• UtilitiesUtilities• image display, rendering, brain extraction, image image display, rendering, brain extraction, image

algebraalgebra• ImplementationImplementation

• ““toolbox” of MATLABtoolbox” of MATLAB®® functions functions• GUIGUI

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

SPM features…SPM features…SPM features…SPM features…

SPM GUI...SPM GUI...SPM GUI...SPM GUI...

SPM resources…SPM resources…SPM resources…SPM resources…

SPM architectureSPM architectureSPM 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,, Mac Mac & & WindowsWindows supported supported– other other UNIXUNIX– disk & memory…disk & memory…

Matlab 6.5 - 7.1Matlab 6.5 - 7.1– 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

NIfTI/Analyze format imagesNIfTI/Analyze 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!!

SPM5 requirements…SPM5 requirements…SPM5 requirements…SPM5 requirements…

SPM CentralSPM Central

SPM documentation…SPM documentation…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

&&SPM5 ManualSPM5 Manual

SPMSPMOnlineOnline

BibliographyBibliography

somesome SPM internet resources… SPM internet resources…somesome SPM internet resources… SPM internet resources…

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

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

<[email protected]><[email protected]>

• FIL neuroscience resources linksFIL neuroscience resources linkshttp://www.fil.ion.ucl.ac.uk/resources.htmlhttp://www.fil.ion.ucl.ac.uk/resources.html

• SPM WikiSPM Wiki

http://en.wikibooks.org/wiki/SPMhttp://en.wikibooks.org/wiki/SPM

• MRC-CBU imagersMRC-CBU imagershttp://www.mrc-cbu.cam.ac.uk/Imaging/Common/http://www.mrc-cbu.cam.ac.uk/Imaging/Common/

SPM CentralSPM Central

SPMwebSPMweb……SPMwebSPMweb……

• Introduction to SPM Introduction to SPM • SPM distribution:SPM distribution:

SPM99, SPM2, SPM5SPM99, SPM2, SPM5• Documentation & Documentation &

BibliographyBibliography• SPM SPM eemail discussion mail discussion

listlist• SPM short courseSPM short course• Example data setsExample data sets• SPM extensionsSPM extensions

• Introduction to SPM Introduction to SPM • SPM distribution:SPM distribution:

SPM99, SPM2, SPM5SPM99, SPM2, SPM5• Documentation & Documentation &

BibliographyBibliography• SPM SPM eemail discussion mail discussion

listlist• SPM short courseSPM short course• Example data setsExample data sets• SPM extensionsSPM extensions

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

SPM – SPM – eemail discussion listmail discussion listSPM – SPM – eemail discussion listmail discussion list

• [email protected]@jiscmail.ac.uk– Web home pageWeb home page

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

– SubscribeSubscribe• http://www.jiscmail.ac.uk/http://www.jiscmail.ac.uk/• eemail mail [email protected]@jiscmail.ac.uk

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

• eemail mail [email protected]@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…

• [email protected]@jiscmail.ac.uk– Web home pageWeb home page

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

– SubscribeSubscribe• http://www.jiscmail.ac.uk/http://www.jiscmail.ac.uk/• eemail mail [email protected]@jiscmail.ac.uk

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

• eemail mail [email protected]@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…

[email protected]@jiscmail.ac.ukhttp://www.fil.ion.ucl.ac.uk/spm/support/http://www.fil.ion.ucl.ac.uk/spm/support/