MATLAB在醫(yī)學(xué)中的應(yīng)用課件

MATLAB在醫(yī)學(xué)中的應(yīng)用MATLAB在醫(yī)學(xué)中的應(yīng)用MATLAB在醫(yī)學(xué)中的應(yīng)用內(nèi)容：1)介紹機(jī)能核磁共振成像技術(shù)

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

SPM(StatisticalParametricMapping)MATLAB在醫(yī)學(xué)中的應(yīng)用機(jī)能核磁共振成像fMRIMATLAB在醫(yī)學(xué)中的應(yīng)用fMRISetup–whatitreallylookslike!MATLAB在醫(yī)學(xué)中的應(yīng)用MagnetSafetyThewhoppingstrengthofthemagnetmakessafetyessential.Thingsfly–Evenbigthings!ScreensubjectscarefullyWereyoueverasoldier?Makesureyouandallyourstudents&staffareawareofhazzards!Developstrategiesforscreeningyourselfeverytimeyouenterthemagnet!MATLAB在醫(yī)學(xué)中的應(yīng)用fMRISetupMATLAB在醫(yī)學(xué)中的應(yīng)用fMRIExperimentStages:Prep1)Preparesubject

ConsentformSafetyscreeningInstructions2)Shimming

puttingbodyinmagneticfieldmakesitnon-uniformadjust3orthogonalweakmagnetstomakemagneticfieldashomogenousaspossible3)Sagittals

TakeimagesalongthemidlinetousetoplanslicesMATLAB在醫(yī)學(xué)中的應(yīng)用fMRIExperimentStages:Anatomical4)Takeanatomical(T1)images

high-resolutionimages(e.g.,1x1x2.5mm)3Ddata:3spatialdimensions,sampledatonepointintime64anatomicalslicestakes~5minutesMATLAB在醫(yī)學(xué)中的應(yīng)用SliceThicknesse.g.,6mmNumberofSlicese.g.,10SAGITTALSLICEIN-PLANESLICEFieldofView(FOV)e.g.,19.2cmVOXEL(VolumetricPixel)3mm3mm6mmSliceTerminologyMatrixSizee.g.,64x64In-planeresolutione.g.,192mm/64=3mmMATLAB在醫(yī)學(xué)中的應(yīng)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(yī)學(xué)中的應(yīng)用StatisticalMapsuperimposedonanatomicalMRIimage~2sFunctionalimagesTimeCondition1Condition2...~5minTimefMRISignal(%change)ROITimeCourseConditionActivationStatisticsRegionofinterest(ROI)MATLAB在醫(yī)學(xué)中的應(yīng)用fMRIPhysicsMATLAB在醫(yī)學(xué)中的應(yīng)用HistoryofNuclearMagneticResonanceNMR=nuclearmagneticresonanceFelixBlochandEdwardPurcell1946:

atomicnucleiabsorband

re-emitradiofrequencyenergy1952:

Nobelprizeinphysicsnuclear:

propertiesofnucleiofatomsmagnetic:

magneticfieldrequiredresonance:interactionbetweenmagneticfieldandradiofrequencyBlochPurcellNMR

MRIMATLAB在醫(yī)學(xué)中的應(yīng)用Physicsofprotons.motionofelectricallychargedparticlesresultsinamagneticforceorthogonaltothedirectionofmotionprotons(nuclearconstituentofatom)haveapropertyofangularmomentumknownasspinAngularmomentum(spin)ofaproton.MATLAB在醫(yī)學(xué)中的應(yīng)用ProtonsaligningwithinamagneticfieldIn“fieldfree”spacerandomlyorientedwhenplacedinamagneticfield(B0;e.g.,ourMRImachines)protonswilleitheralignwiththemagneticfieldororthogonaltoit(processofreachingmagneticequilibrium)thereisasmalldifference(10:1million)inthenumberofprotonsinthelowandhighenergystates–withmoreinthelowstateleadingtoanetmagnetization(M)InsidemagneticfieldorientedwithoragainstB0M=netmagnetizationMAppliedMagneticField(B0)MATLAB在醫(yī)學(xué)中的應(yīng)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(yī)學(xué)中的應(yīng)用ReadingM0RFcoilsreceivethenetmagnetizationfromtheobjectplacedwithinthecoil(e.g.,asubject’shead)canalsohavesend/receiveRFcoilsthatalsodelivertheRFpulse(togettheswinggoing)–usuallythepulseisdeliveredbygradientcoilsMATLAB在醫(yī)學(xué)中的應(yīng)用MagnetRFCoilRFCoil4TmagnetUltrashortMRphysicsoverviewsource:MATLAB在醫(yī)學(xué)中的應(yīng)用Step1:PutSubjectinBigMagnetProtons(hydrogenatoms)have“spins”(liketops).Theyhaveanorientationandafrequency.Whenyouputamaterial(likeyoursubject)inanMRIscanner,someoftheprotonsbecomeorientedwiththemagneticfield.MATLAB在醫(yī)學(xué)中的應(yīng)用source:Step2:ApplyRadioWavesWhenyouapplyradiowaves(RFpulse)attheappropriatefrequency,youcanchangetheorientationofthespinsastheprotonsabsorbenergy.Afteryouturnofftheradiowaves,astheprotonsreturntotheiroriginalorientations,theyemitenergyintheformofradiowaves.MATLAB在醫(yī)學(xué)中的應(yīng)用Step3:MeasureRadioWavesT1measureshowquicklytheprotonsrealignwiththemainmagneticfieldT2measureshowquicklytheprotonsgiveoffenergyastheyrecovertoequilibriumfathashighsignalbrightCSFhaslowsignaldarkT1-WEIGHTEDANATOMICALIMAGET2-WEIGHTEDANATOMICALIMAGEfathaslowsignaldarkCSFhashighsignalbrightMATLAB在醫(yī)學(xué)中的應(yīng)用sinusesearcanalsThisisusuallynotsonice,but...WealsohaveT2*weightedimages:thesearesensitivetolocalmagneticfieldinhomogeneities.TheseT2*weightedimageshaveartifactsnearjunctionsbetweenairandtissue:sinuses,earcanalsMATLAB在醫(yī)學(xué)中的應(yīng)用TheBOLDContrastBOLD(BloodOxygenationLevelDependent)contrast=measuresinhomogeneitiesinthemagneticfieldduetochangesinthelevelofO2inthebloodOxygenatedblood?Non-magneticNosignalloss…Deoxygenatedblood?Magnetic!Signalloss!!!MATLAB在醫(yī)學(xué)中的應(yīng)用BOLDsignalneuralactivitybloodflow

oxyhemoglobin

T2*

MRsignalRESTACTIVITYMATLAB在醫(yī)學(xué)中的應(yīng)用TheHaemodynamicResponseFunction(HRF)MATLAB在醫(yī)學(xué)中的應(yīng)用PhysiologyoftheBOLDsignalMATLAB在醫(yī)學(xué)中的應(yīng)用BOLDseemstobecorrelatedtopostsynapticactivityBOLDseemstoreflecttheinputofacorticalareaaswellasitsintracorticalprocessingMATLAB在醫(yī)學(xué)中的應(yīng)用

HowdoestheBOLDreflecttheenergydemandsofthebrain?MATLAB在醫(yī)學(xué)中的應(yīng)用SPM(StatisticalParametricMapping)MATLAB在醫(yī)學(xué)中的應(yīng)用StatisticalParametricMapping…avoxelbyvoxelhypothesistestingapproachreliablyidentifyregionsshowinga

significantexperimentaleffectofinterestTypeIerrorsignificancetestateachvoxelmodelvoxeldata,testparametersnoexactprioranatomicalhypothesismultiplecomparisonsGeneralLinearModelRandomfieldtheorySPM…thesoftwareWhatisSPM?

thegameofthenameStatisticalParametricMappingreferstotheconstructionandassessmentofspatiallyextendedstatisticalprocessusedtotesthypothesesabout[neuro]imagingdatafromSPECT/PET&fMRI.

TheseideashavebeeninstantiatedinsoftwarethatiscalledSPM.“”MATLAB在醫(yī)學(xué)中的應(yīng)用SPM’99GUI…MATLAB在醫(yī)學(xué)中的應(yīng)用Spatialrealignment,spatialnormalisation,segmentation,coregistration,spatialsmoothingStatisticalvoxelbyvoxelstatisticalanalysisgenerallinearmodel,generalisedfortemporalautocorrelationrandomeffectsanalysesmultiplecomparisons:Correctedp-valuesfromrandomfieldtheoryplotting&resultsinterrogationUtilitiesimagedisplay,CheckReg,rendering,brainextraction,adjustedmeans,imagealgebraSPMfeatures…MATLAB在醫(yī)學(xué)中的應(yīng)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(yī)學(xué)中的應(yīng)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(yī)學(xué)中的應(yīng)用WorkstationdevelopedonSunSolarisUNIXSolaris,Linux&WindowssupportedotherUNIXdisk&memory…Matlab5.3.0orlaternospecial“toolboxes”requiredSPM’99won’tworkwithMatlab4ANSIICCompilertocompileexternalC–mexroutinesreadyforSolaris,Linux,&WindowsAnalyze/MINCformatimagesconversionprogramextendSPMInternetaccess…forSPMweb&theemaildiscussionlistPlentyoftime!SPM’99requirements…MATLAB在醫(yī)學(xué)中的應(yīng)用SPMresources…MATLAB在醫(yī)學(xué)中的應(yīng)用SPMdocumentation…peerreviewedliteratureSPMcoursenotes,

HumanBrainFunction& SPMmanualonlinehelp&

functiondescriptionsalgorithmdescriptions,

codeannotations,

pseudo-codeMATLAB在醫(yī)學(xué)中的應(yīng)用SPMwebsiteSPMemaildiscu