MATLAB在醫學中的應用MATLAB在醫學中的應用MATLAB在醫學中的應用內容：1)介紹機能核磁共振成像技術

（fMRI:functionalMagneticResonanceImaging)２)介紹MATLAB上開發的fMRI分析軟件

SPM(StatisticalParametricMapping)MATLAB在醫學中的應用機能核磁共振成像fMRIMATLAB在醫學中的應用fMRISetup–whatitreallylookslike!MATLAB在醫學中的應用MagnetSafetyThewhoppingstrengthofthemagnetmakessafetyessential.Thingsfly–Evenbigthings!ScreensubjectscarefullyWereyoueverasoldier?Makesureyouandallyourstudents&staffareawareofhazzards!Developstrategiesforscreeningyourselfeverytimeyouenterthemagnet!MATLAB在醫學中的應用fMRISetupMATLAB在醫學中的應用fMRIExperimentStages:Prep1)Preparesubject

ConsentformSafetyscreeningInstructions2)Shimming

puttingbodyinmagneticfieldmakesitnon-uniformadjust3orthogonalweakmagnetstomakemagneticfieldashomogenousaspossible3)Sagittals

TakeimagesalongthemidlinetousetoplanslicesMATLAB在醫學中的應用fMRIExperimentStages:Anatomical4)Takeanatomical(T1)images

high-resolutionimages(e.g.,1x1x2.5mm)3Ddata:3spatialdimensions,sampledatonepointintime64anatomicalslicestakes~5minutesMATLAB在醫學中的應用SliceThicknesse.g.,6mmNumberofSlicese.g.,10SAGITTALSLICEIN-PLANESLICEFieldofView(FOV)e.g.,19.2cmVOXEL(VolumetricPixel)3mm3mm6mmSliceTerminologyMatrixSizee.g.,64x64In-planeresolutione.g.,192mm/64=3mmMATLAB在醫學中的應用fMRIExperimentStages:Functional5)Takefunctional(T2*)images

imagesareindirectlyrelatedtoneuralactivityusuallylowresolutionimages(3x3x5mm)allslicesatonetime=avolume(sometimesalsocalledanimage)samplemanyvolumes(timepoints)(e.g.,1volumeevery2secondsfor150volumes=300sec=5minutes)4Ddata:3spatial,1temporalfirstvolume(2sectoacquire)…MATLAB在醫學中的應用StatisticalMapsuperimposedonanatomicalMRIimage~2sFunctionalimagesTimeCondition1Condition2...~5minTimefMRISignal(%change)ROITimeCourseConditionActivationStatisticsRegionofinterest(ROI)MATLAB在醫學中的應用fMRIPhysicsMATLAB在醫學中的應用HistoryofNuclearMagneticResonanceNMR=nuclearmagneticresonanceFelixBlochandEdwardPurcell1946:

atomicnucleiabsorband

re-emitradiofrequencyenergy1952:

Nobelprizeinphysicsnuclear:

propertiesofnucleiofatomsmagnetic:

magneticfieldrequiredresonance:interactionbetweenmagneticfieldandradiofrequencyBlochPurcellNMR

MRIMATLAB在醫學中的應用Physicsofprotons.motionofelectricallychargedparticlesresultsinamagneticforceorthogonaltothedirectionofmotionprotons(nuclearconstituentofatom)haveapropertyofangularmomentumknownasspinAngularmomentum(spin)ofaproton.MATLAB在醫學中的應用ProtonsaligningwithinamagneticfieldIn“fieldfree”spacerandomlyorientedwhenplacedinamagneticfield(B0;e.g.,ourMRImachines)protonswilleitheralignwiththemagneticfieldororthogonaltoit(processofreachingmagneticequilibrium)thereisasmalldifference(10:1million)inthenumberofprotonsinthelowandhighenergystates–withmoreinthelowstateleadingtoanetmagnetization(M)InsidemagneticfieldorientedwithoragainstB0M=netmagnetizationMAppliedMagneticField(B0)MATLAB在醫學中的應用LarmorFrequencyLarmorequation

f=B0 =42.58MHz/T At1.5T,f=63.76MHz At4T,f=170.3MHzFieldStrength(Tesla)ResonanceFrequencyfor1H170.363.81.54.0theenergydifferencebetweenthehigh(orientedwithB0)andlow(orientedagainstB0)energyprotonsismeasurableandisexpressedintheLarmorequationMATLAB在醫學中的應用ReadingM0RFcoilsreceivethenetmagnetizationfromtheobjectplacedwithinthecoil(e.g.,asubject’shead)canalsohavesend/receiveRFcoilsthatalsodelivertheRFpulse(togettheswinggoing)–usuallythepulseisdeliveredbygradientcoilsMATLAB在醫學中的應用MagnetRFCoilRFCoil4TmagnetUltrashortMRphysicsoverviewsource:MATLAB在醫學中的應用Step1:PutSubjectinBigMagnetProtons(hydrogenatoms)have“spins”(liketops).Theyhaveanorientationandafrequency.Whenyouputamaterial(likeyoursubject)inanMRIscanner,someoftheprotonsbecomeorientedwiththemagneticfield.MATLAB在醫學中的應用source:Step2:ApplyRadioWavesWhenyouapplyradiowaves(RFpulse)attheappropriatefrequency,youcanchangetheorientationofthespinsastheprotonsabsorbenergy.Afteryouturnofftheradiowaves,astheprotonsreturntotheiroriginalorientations,theyemitenergyintheformofradiowaves.MATLAB在醫學中的應用Step3:MeasureRadioWavesT1measureshowquicklytheprotonsrealignwiththemainmagneticfieldT2measureshowquicklytheprotonsgiveoffenergyastheyrecovertoequilibriumfathashighsignalbrightCSFhaslowsignaldarkT1-WEIGHTEDANATOMICALIMAGET2-WEIGHTEDANATOMICALIMAGEfathaslowsignaldarkCSFhashighsignalbrightMATLAB在醫學中的應用sinusesearcanalsThisisusuallynotsonice,but...WealsohaveT2*weightedimages:thesearesensitivetolocalmagneticfieldinhomogeneities.TheseT2*weightedimageshaveartifactsnearjunctionsbetweenairandtissue:sinuses,earcanalsMATLAB在醫學中的應用TheBOLDContrastBOLD(BloodOxygenationLevelDependent)contrast=measuresinhomogeneitiesinthemagneticfieldduetochangesinthelevelofO2inthebloodOxygenatedblood?Non-magneticNosignalloss…Deoxygenatedblood?Magnetic!Signalloss!!!MATLAB在醫學中的應用BOLDsignalneuralactivitybloodflow

oxyhemoglobin

T2*

MRsignalRESTACTIVITYMATLAB在醫學中的應用TheHaemodynamicResponseFunction(HRF)MATLAB在醫學中的應用PhysiologyoftheBOLDsignalMATLAB在醫學中的應用BOLDseemstobecorrelatedtopostsynapticactivityBOLDseemstoreflecttheinputofacorticalareaaswellasitsintracorticalprocessingMATLAB在醫學中的應用

HowdoestheBOLDreflecttheenergydemandsofthebrain?MATLAB在醫學中的應用SPM(StatisticalParametricMapping)MATLAB在醫學中的應用StatisticalParametricMapping…avoxelbyvoxelhypothesistestingapproachreliablyidentifyregionsshowinga

significantexperimentaleffectofinterestTypeIerrorsignificancetestateachvoxelmodelvoxeldata,testparametersnoexactprioranatomicalhypothesismultiplecomparisonsGeneralLinearModelRandomfieldtheorySPM…thesoftwareWhatisSPM?

thegameofthenameStatisticalParametricMappingreferstotheconstructionandassessmentofspatiallyextendedstatisticalprocessusedtotesthypothesesabout[neuro]imagingdatafromSPECT/PET&fMRI.

TheseideashavebeeninstantiatedinsoftwarethatiscalledSPM.“”MATLAB在醫學中的應用SPM’99GUI…MATLAB在醫學中的應用Spatialrealignment,spatialnormalisation,segmentation,coregistration,spatialsmoothingStatisticalvoxelbyvoxelstatisticalanalysisgenerallinearmodel,generalisedfortemporalautocorrelationrandomeffectsanalysesmultiplecomparisons:Correctedp-valuesfromrandomfieldtheoryplotting&resultsinterrogationUtilitiesimagedisplay,CheckReg,rendering,brainextraction,adjustedmeans,imagealgebraSPMfeatures…MATLAB在醫學中的應用SPMhistory…SPMclassic:in-housesoftware@MRC-CUbyKarl

Friston&JonHeather

releasedtotheemergingfunctional

neuroimagingcommunityin1991whyfreelydistribute?communityopenpromoterigour(inemergingfield)promotecollaborationcommonanalysisframeworkSPM94+(SPM95,SPM96,SPM99…)developedunderauspicesofthe

WellcomeDepartmentofCognitiveNeurologycompletelyrewrittenprimaryauthorsKarlFriston,JohnAshburner,AndrewHolmes,Jean-BaptistePolinekeycollaboratorKeithWorsleyGUIsupportSPMweb,SPMhelp,SPMcourseSPMtoolboxesSnPMMultivariateunwarpMATLAB在醫學中的應用SPMarchitectureSPMMatLabfunctions&scripts ?basic“toolbox”functions?macrofunctions/scripts

?GUIfunctions&i/oprimitivesexternallylinkedC-code ?intensiveoperations?memorymappingplatform ?MatLabonUNIX,Linux,WindowsMatLab:4thGenerationlanguage ?highlevelmatrixbasedengineeringmathslanguage

?basicdatatypeismatrix?mathematicalsyntaxinterpretedenvironmentgraphics&GUIprimitivesprovidedprogramming ?scripts?functions(cancompile)?objects?linkedC/C++MATLAB在醫學中的應用WorkstationdevelopedonSunSolarisUNIXSolaris,Linux&WindowssupportedotherUNIXdisk&memory…Matlab5.3.0orlaternospecial“toolboxes”requiredSPM’99won’tworkwithMatlab4ANSIICCompilertocompileexternalC–mexroutinesreadyforSolaris,Linux,&WindowsAnalyze/MINCformatimagesconversionprogramextendSPMInternetaccess…forSPMweb&theemaildiscussionlistPlentyoftime!SPM’99requirements…MATLAB在醫學中的應用SPMresources…MATLAB在醫學中的應用SPMdocumentation…peerreviewedliteratureSPMcoursenotes,

HumanBrainFunction& SPMmanualonlinehelp&

functiondescriptionsalgorithmdescriptions,

codeannotations,

pseudo-codeMATLAB在醫學中的應用SPMwebsiteSPMemaildiscu