Post on 28-Mar-2015
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/
<spm@jiscmail.ac.uk><spm@jiscmail.ac.uk>
• 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
• spm@jiscmail.ac.ukspm@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 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.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 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/support/http://www.fil.ion.ucl.ac.uk/spm/support/