Post on 21-May-2022
Quality control in fMRI
Scott Peltier Krisanne Litinas Functional MRI Laboratory
Along with: Alex Iordan, Psychology Mike Angstadt, Psychiatry
Overview
• Alwaysexaminedata!Ina4melymanner!– Verifythatalldataexists(imagingandother)– Quicklycatchanyacquisi4on/protocolproblems,andiden4fyindividualoutliers(suchasexcessivemo4on,notaskresponse,etc)
Visual inspec,on
• Itisagoodprac4cetovisuallyinspect:
• rawdata• outputsofeachpreprocessingstep
• individualandgroup-levelsignalintensitymasks
Individualsubjectsmasks
Group-levelmask
A.D.Iordan
Files/toolsforinspec4on
• Imagingfiles,processingoutput– Bothfunc4onalandanatomical
• Favoriteimage/movieviewer– FSL,SPM,Matlab,AFNI,etc
• Otherpackages– ICA,Compcor,ART
• Hands-onworkshops?
QAexamples
• Anatomy– Homogeneitycorrec4on– Skullstripping
• Func4onal– Rtprun(realignment,slice4ming,physionoise)– despiking– fieldmapcorrec4on– imagereconstruc4on
Homogeneitycorrec4on• Watchfortoobright/toodarkaYercorrec4on
Fail on brainstem
Before After
Skullstripping
• WatchfortooliZle/toomuch
Loss of tissue
Before After
Headmo4on
• Inspect:mo4onparametersfile,movie• Correct:realigment,mo4onparametersasregressors
• Addi4onal:Maximumthresholdsforsubjectinclusion;scrubbing
SampleMovementParameters
Headmo4on
• Showmovie
ART–LiZleMo4onA.D. Iordan
ART–Substan4alMo4onA.D. Iordan
Slice4mingcorrec4on
• Verifyatstudystart:sliceacquisi4onorder– Ascending/Descending– Sequen4al/Interleaved– Regular/Mul4band
• Inspect:Preprocessingoutput,resultsacrossslices
Slice-4ming
• Robertexamples
Note: sequential ascending
Welsh, Hardee, Peltier. ‘Slice-time correction in resting-state (and fMRI) gone bad’, HBM2014.
Slice-4ming
Slice-4ming
• RobertExtra
Flex.pdf
Physiologicalnoise
• Inspect:Timecourse,rawtraces,variancemapsbeforeandaYer
• Addi4onal:Task/correla4onmaps
Physionoise:Timecourses
Time domain
Frequency domain
courtesy of Douglas Noll
Inte
nsity
Image number
Timecourse before (purple) and after (black) regression correction.
Physionoise
Flex.pdf example
Physio Data: Raw Traces
Good Bad
A.D. Iordan
Despiking
• Inspect:Preprocessingoutput,slice/globalsignal4mecoursedifferences,movies
White Pixel Artifact
• Caused by a noise spike during acquisition• Spike in K-space <--> sinusoid in image
space
Ques4ons?
Fieldmapcorrec4ons
• Suscep4bility-inducedsignalloss
• Geometricdistor4ons
warped epi image unwarped epi image field map high res image
Field map correction: EPI Multiband
Before M.Angstadt
Field map correction: EPI Multiband
After M.Angstadt
Fieldmapcorrec4on:EPI
• CurrentlyworkingonitwithMike• Willimplementitforbothmul4bandandstandardfieldmaps,inves4gateSPMandFSL
• Willhaveop4oninstream
Fieldmapcorrecton:Spiral
• Fieldmapbuilt-in,fieldmapcorrec4onisstandardinprocessingstream(yay!)– Some4mesfieldmapsgowrong(boo!)
Standardfieldmapcorrec4onNo correction Standard field map
correction
Iterative recon -Iterative recon updates image estimates -Increases recon time by at least 5x
Standard Iterative
Itera4vereconwithoffsetfieldmap-Sometimes fieldmaps are incorrect -In this case, we can estimate correction factor to get new field map, then apply iterative recon
Standard Iterative w/ offset
Artifact Type: Flares/Blow-out
Original Recon Iterative Recon Iterative Recon + Offset Correction
A.D.Iordan
Artifact Type: Ripples
Original Recon Iterative Recon Iterative Recon + Offset Correction
A.D.Iordan
Artifact Type: Signal Loss (Temporal)
Original Recon Iterative Recon Iterative Recon + Offset Correction
A.D.Iordan
Itrecon/offset fieldmap
• Work in progress • Contact us with questions