spmintroduction scott peltier fmri laboratory university of michigan slides adapted from t. nichols

SPMSPMIntroductionIntroduction

Scott PeltierScott Peltier

FMRI LaboratoryFMRI LaboratoryUniversity of MichiganUniversity of Michigan

Slides adapted from T. NicholsSlides adapted from T. Nichols

SPM!SPM!

Software to perform computation, Software to perform computation, manipulation and display of imaging datamanipulation and display of imaging data

SPM : OverviewSPM : Overview• Library of MATLAB and C functionsLibrary of MATLAB and C functions

• Graphical user interfaceGraphical user interface

• Four main components:Four main components:– PreprocessingPreprocessing– Model Specification & FittingModel Specification & Fitting– Inference & Results InterrogationInference & Results Interrogation– Supplemental ToolsSupplemental Tools

SPM: PreprocessingSPM: Preprocessing• Eliminate systematic variation before Eliminate systematic variation before

statistical modelingstatistical modeling

• Slice timingSlice timing– Adjust for variable acquisition time over slicesAdjust for variable acquisition time over slices– In UM processing stream, this is already doneIn UM processing stream, this is already done

• ““RealignRealign””mentment– Intrasubject registrationIntrasubject registration– Motion correctionMotion correction– Done in UM streamDone in UM stream

slice 1

slice 4

TR 2TR 3TR

time

SPM: PreprocessingSPM: Preprocessing• ““CoregisterCoregister””ationation

– Intrasubject, intermodality registrationIntrasubject, intermodality registration– Registration of MR imagesRegistration of MR images

with different TR/TEwith different TR/TE

• Spatial Spatial ““NormalizeNormalize””ationation– Intersubject registrationIntersubject registration– Register subject anatomy to atlas spaceRegister subject anatomy to atlas space

SPM SPM T1 templateT1 templateMNI spaceMNI space

SPM: PreprocessingSPM: Preprocessing• Spatial Spatial ““SmoothSmooth””inging

– Blur data into submission…Blur data into submission…• To satisfy random field theory assumptionsTo satisfy random field theory assumptions

• For intersubject analysesFor intersubject analyses

• ““SegmentSegment””ation into GM/WM/CSFation into GM/WM/CSF– Usually not directly usedUsually not directly used– Useful for structural studiesUseful for structural studies

Before Before convolutionconvolution

Convolved Convolved w/ circlew/ circle

Convolved Convolved w/ Gaussianw/ Gaussian

Adapted from SPM course slidesAdapted from SPM course slides

SPM: Model SpecificationSPM: Model Specification• ““Specify 1st-levelSpecify 1st-level””

– Specify the design, creating SPM.matSpecify the design, creating SPM.mat

• ““Specify 2nd-levelSpecify 2nd-level””– T-tests (One or two sample, paired)T-tests (One or two sample, paired)

– RegressionRegression

• ““ReviewReview””– Examine correlation of predictorsExamine correlation of predictors

– Power spectrum of experimental effectsPower spectrum of experimental effects

• ““EstimateEstimate””– Fit a specified model Fit a specified model

based on a SPM.mat filebased on a SPM.mat file

SPM: InferenceSPM: Inference• ““ ResultsResults”” button button

• First brings up First brings up ““Contrast ManagerContrast Manager””Can define single (t) Can define single (t)

or sets (F) of contrastsor sets (F) of contrasts

• Then displays MIPThen displays MIP– MIP = Maximum Intensity ProjectionMIP = Maximum Intensity Projection– Glass BrainGlass Brain– Can Can ““surfsurf”” by dragging cursor by dragging cursor

SPM: InferenceSPM: Inference• Interactive windowInteractive window

– p-valuesp-values• Correced for whole brain or subregionCorreced for whole brain or subregion

– Plotting of time coursesPlotting of time courses– ““OverlaysOverlays””

• Superimpose results on other imagesSuperimpose results on other images

– Current location and valueCurrent location and value

SPM: Miscellaneous ToolsSPM: Miscellaneous Tools

• ““DisplayDisplay””– Displays image Displays image

with orthogonal sectionswith orthogonal sections– Check intensity valuesCheck intensity values– Change originChange origin– Change world spaceChange world space

• i.e. Apply rotations/translationsi.e. Apply rotations/translations

SPM: Miscellaneous ToolsSPM: Miscellaneous Tools

• ““Check RegCheck Reg””– Display multiple imagesDisplay multiple images– Essential tool for assessing Essential tool for assessing

alignment of imagesalignment of images– All images are displayed in the All images are displayed in the

space of the first imagespace of the first image

SPM: Miscellaneous ToolsSPM: Miscellaneous Tools• ““ImCalcImCalc””

– Image calculatorImage calculator– Give one or more images, perform MATLAB Give one or more images, perform MATLAB

arithmetic and write out resultarithmetic and write out result

• ““UtilsUtils””– Change directoryChange directory

• Results are written to current directory!Results are written to current directory!

– Delete files, etc.Delete files, etc.

SPM8 Batch EditorSPM8 Batch Editor

• Allows jobs to be saved, Allows jobs to be saved,

re-loaded, changedre-loaded, changed

• Helps remove Helps remove ““Oops!Oops!”” factor factor

• Multiple steps can be loaded, Multiple steps can be loaded,

run at oncerun at once

SPM: PerspectiveSPM: Perspective• SPM tries to be a single solution for all fMRI SPM tries to be a single solution for all fMRI

processing and analysis, but there can be no processing and analysis, but there can be no such thing!such thing!– FMRI is a rapidly evolving field where each FMRI is a rapidly evolving field where each

dataset has huge number of observations!dataset has huge number of observations!

• DonDon’’t let SPM be a black box!t let SPM be a black box!• Understand what each component doesUnderstand what each component does• Understand how to get at the dataUnderstand how to get at the data

– e.g. using e.g. using ‘‘DisplayDisplay’’, , ‘‘Check RegCheck Reg’’

ResourcesResources

• SPMSPMwebweb site: site: http://www.fil.ion.ucl.ac.uk/spm/http://www.fil.ion.ucl.ac.uk/spm/• Introduction to SPM Introduction to SPM

• SPM code download: SPM99, SPM2, SPM5, SPM8SPM code download: SPM99, SPM2, SPM5, SPM8

• Documentation & BibliographyDocumentation & Bibliography

• SPM short courseSPM short course

• Example data setsExample data sets

• SPM extensionsSPM extensions

• SPM SPM eemail discussion listmail discussion list

• Other software packages can complement SPMOther software packages can complement SPM– MRIcronMRIcron:: http://www.mccauslandcenter.sc.edu/mricro/mricron/index.htmlhttp://www.mccauslandcenter.sc.edu/mricro/mricron/index.html

– Quick and easy to read, display, and convert image dataQuick and easy to read, display, and convert image data

AlternativesAlternatives• FSL: FSL: http://www.fmrib.ox.ac.uk/fslhttp://www.fmrib.ox.ac.uk/fsl

• Open sourceOpen source

• Comprehensive tools for FMRI and DTI, has nice ICA analysis tool Comprehensive tools for FMRI and DTI, has nice ICA analysis tool

(MELODIC)(MELODIC)

• FreeFree

• AFNI: AFNI: http://afni.nimh.nih.govhttp://afni.nimh.nih.gov

• Open sourceOpen source

• Active community, multiple pluginsActive community, multiple plugins

• FreeFree

• BrainVoyager: BrainVoyager: http://www.brainvoyager.comhttp://www.brainvoyager.com

• Excellent visualizationExcellent visualization

• Closed source, ~$5kClosed source, ~$5k

SPMSPMSpatial TransformationsSpatial Transformations

Imaging data formatsImaging data formats• Analyze formatAnalyze format

– .img Raw, binary data; 3D or 4D.img Raw, binary data; 3D or 4D– .hdr Small binary header.hdr Small binary header

• Image dimensionImage dimension

• Voxel sizeVoxel size

• NIFTI formatNIFTI format– .img + .hdr.img + .hdr– Like Analyze, but different .hdr definitionLike Analyze, but different .hdr definition– .nii .nii Single file! Single file! Header and Image file concatenatedHeader and Image file concatenated– World space transformation coded in NIFTI headerWorld space transformation coded in NIFTI header

Is Left Right?Is Left Right?• Two conventions for viewing imagesTwo conventions for viewing images

– NeurologicalNeurological• On the screen, Left is Left side of subjectOn the screen, Left is Left side of subject• As if standing behind the head of the patientAs if standing behind the head of the patient

– RadiologicalRadiological• On the screen, Left is Right side of subjectOn the screen, Left is Right side of subject• As if standing at the foot of the patientAs if standing at the foot of the patient

• Standard in clinical radiology is, um, radiologicalStandard in clinical radiology is, um, radiological

• SPM always uses Neurological conventionSPM always uses Neurological convention– Default for Analyze set by defaults.analyze.flip in spm defaults.mDefault for Analyze set by defaults.analyze.flip in spm defaults.m

• flip = 0 ,Neuro., flip = 1 ,Rad.flip = 0 ,Neuro., flip = 1 ,Rad.• NIFTI images NIFTI images allegedly allegedly have no ambiguity about left & righthave no ambiguity about left & right

LL

RR

RR

LL

NoseNose

Coregister & realignmentCoregister & realignment• Coregistration & Realignment are rigid body Coregistration & Realignment are rigid body

transformationstransformations– SubjectSubject’’s head doesns head doesn’’t change size or warp between scanst change size or warp between scans– Well, actually...Well, actually...

• Each requires a Each requires a ““ReferenceReference”” and a and a ““SourceSource””– Reference: Fixed imageReference: Fixed image– Source: Image that is transformedSource: Image that is transformed

• SPM modifies the .hdr file of the SPM modifies the .hdr file of the object object imageimage– Unless you explicitly ask it to, it doesnUnless you explicitly ask it to, it doesn’’t write out an imaget write out an image– Saves lots of disk space!Saves lots of disk space!

Voxel space vs. world spaceVoxel space vs. world space• Voxel SpaceVoxel Space

– Just the original imageJust the original image– No reorientations or flipsNo reorientations or flips

• World SpaceWorld Space– Space defined by transformation from voxel to mm Space defined by transformation from voxel to mm

matrix Mmatrix M• Let v be a voxel location indexed from (1,1,1)Let v be a voxel location indexed from (1,1,1)• Then w=M*[v;1] is that location in world space, in mmThen w=M*[v;1] is that location in world space, in mm• Can represent rotations, translations and flipsCan represent rotations, translations and flips

Functional imagesraprun_01.nii

Low-res anatomyt1overlay.nii

High-res anatomyt1spgr.nii

Functional Space

Data Fresh from fMRI LabData Fresh from fMRI Lab

Template imageT1.nii

scalped_avg152T1.nii

MNI Atlas Space

CoregistrationCoregistration

SourceReference

Coregister button

Sets new world space in NIFTI headerDetermined from: Rigid body, M.I. registration of high-res to low-res anatomy

Functional Space






MNI Atlas Space

Functional Space

After CoregistrationAfter Coregistration





MNI Atlas Space


(NIFTI header)

Normalize button

Creates _sn.mat file

Determined from: Nonlinear, L.S. registration of high-res anatomy to T1 MNI template

Functional Space

Spatial NormalisationSpatial Normalisation





MNI Atlas Space


(NIFTI header)

Functional Space

Spatial NormalisationSpatial Normalisation

_sn.mat file maps any

Functional Space image to MNI space!

MNI Atlas Space






(NIFTI header)

Functional Space

After After ““Writing NormalizedWriting Normalized””

Functional Space

MNI Atlas Space






(NIFTI header)

Normalized imageswt1spgr.nii

wraprun_01.nii

rap_run’s

Functional Space

MNI Atlas Space

Group Analysis: Strategy 1Group Analysis: Strategy 1Only transform contrast imgOnly transform contrast img’’ss

wcon’s

beta’scon’s

spmT’s

Intrasubjectanalysis result

Intrasubject analysis contrast images,transformed into atlas space (w/ _sn.mat),ready for group analysis

_sn.mat

rap_img’s

Functional Space

MNI Atlas Space

Group Analysis: Strategy 2Group Analysis: Strategy 2Transform all functionalsTransform all functionals

beta’scon’s

spmT’s

Intrasubjectanalysis result

con images ready for group analysis (already in atlas space)

wrap_run’s

All functionaldata transformed into atlas space (w/ _sn.mat)

_sn.mat

Normalisation recommendationsNormalisation recommendations

• With With ‘‘scalpedscalped’’ brains use brains use ‘‘scalpedscalped’’ template template– Scalped template Scalped template scalped_avg152T1.niiscalped_avg152T1.nii– Should Should give best resultsgive best results

• We donWe don’’t care about scalp alignment!t care about scalp alignment!

• Make sure WM equal in brightnessMake sure WM equal in brightness– T1T1’’s can have inhomogeneity artifact, where center of s can have inhomogeneity artifact, where center of

volume is brightervolume is brighter– Should apply homogeneity correction (bias correction)Should apply homogeneity correction (bias correction)– UM: make sure to UM: make sure to use use hheet1spgr, t1spgr, hhet1overlayet1overlay

spmintroduction scott peltier fmri laboratory university of michigan slides adapted from t. nichols

Documents

image slide

file slide

spm course slides slide

value slide

cursor slide

rotationstranslations

nichols slide

tr 2tr3tr time slide