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