High Fidelity Brain Connectivity Imaging...Todd Harshbarger Ana Batrachenko Trong-Kha Truong NS 041328, EB 009483, NS 075017 Acknowledgement Faculty and Staff at the Duke – UNC Brain

CNI Inauguration WorkshopStanford, March 22nd, 2012

Allen W. Song, PhDBrain Imaging and Analysis Center

Duke University

High Fidelity Brain Connectivity Imaging-Recent Progress on Diffusion Weighted MRI

for High Resolution and Low Distortion

The Need for High Resolution and Low Distortion to Image Connectivity

Brain as an Example:Brain as an Example:

>100 Billion Neurons>100 Billion Neurons

>1 Trillion Connections>1 Trillion Connections

>7 Billions Brains>7 Billions Brains

What Resolution Should We Reach with Diffusion Weighted MRI?

High Spatial ResolutionHigh Spatial ResolutionIs Needed for UIs Needed for U--fibersfibers

High Angular ResolutionHigh Angular ResolutionSolves Crossing Fibers withoutSolves Crossing Fibers withoutDemand on Spatial ResolutionDemand on Spatial Resolution

2 mm into WM0diamagnetic paramagnetic

1 mm into WM0diamagnetic paramagnetic

WM/GM Interface0diamagnetic paramagnetic

1 mm into GM0diamagnetic paramagnetic




What Resolution Should We Reach with Diffusion Weighted MRI?

HighHigh--ResolutionResolutionSusceptibility ImagingSusceptibility ImagingGuidonGuidon, Liu, et al., Duke, Liu, et al., Duke

Benefit of High-Resolution Diffusion MRI

ROIs 1x1x1 mm3 2x2x2 mm3 3x3x3 mm3

1 mm3

2x2x2 mm2x2x2 mm3 1x1x1 mm1x1x1 mm3

High-Res FA

High-Resolution DTILiu et al., Duke

Benefit of High-Resolution Diffusion MRI

High-Resolution DTIGuidon et al., Duke

3x3x3mm3 2x2x2mm3 1x1x1mm30

0.8RegionRegion

1111 234234

234234

FAFA

High Resolution DWI Is Not So Easy ….At the present time, the only viable solution to achieve At the present time, the only viable solution to achieve highhigh--resolution DWI is through resolution DWI is through multi-shot acquisition

TwoTwo--shot DW EPIshot DW EPI TwoTwo--shot DW Spiralshot DW Spiral

Self-Navigated Interleaved Spiral (SNAILS)To Remove Aliasing Artifacts

Liu et al., BIAC, Duke University

bo b1 b2Baseline Image Diffusion Weighting Images

…

…

But it requires specialized pulse sequence,But it requires specialized pulse sequence,as well as additional scan and reconstruction timeas well as additional scan and reconstruction time

Goal: To develop efficient, effective, and practical To develop efficient, effective, and practical acquisition/reconstruction methods for highacquisition/reconstruction methods for high--fidelity DWI.fidelity DWI.

Criteria:Ideally, the methodology should require Ideally, the methodology should require minimal pulse sequence changes, remove the minimal pulse sequence changes, remove the need for additional reference scans, and still need for additional reference scans, and still result in highresult in high--quality DW images.quality DW images.

Cycling-Phase Reconstruction (CPR)

A general postA general post--processing framework designed to processing framework designed to correct for hardwarecorrect for hardware-- and subjectand subject--induced aliasing induced aliasing artifacts in accelerated MRI scans (EPI, Spiral, artifacts in accelerated MRI scans (EPI, Spiral, Propeller, FSE, GRASE among others), without Propeller, FSE, GRASE among others), without reference scansreference scans

Also applicable to diffusion weighted singleAlso applicable to diffusion weighted single--shot / shot / multimulti--shot / parallel EPI, Spiral, and Propeller shot / parallel EPI, Spiral, and Propeller acquisitions, without reference scansacquisitions, without reference scans

Chen et al.,Magn Reson Med. 2011 Oct;66(4):1057-66

CPR for 2D EPI

IntensityIntensityProfileProfile

SortedSortedProfileProfile

CostCostFunctionFunction


CPR for 2D EPI


11--ShotShot

22--ShotShot

33--ShotShot

44--ShotShotEPIEPI

No CorrectionNo Correction 11--D ReferenceD Reference CPR

Can CPR Work in Spiral Imaging ?

a: b=0 image

b: image (a)with simulatedphase error

c: image (b)reconstructedby cyclingphases with different φ0and gx values

d: backgroundenergy in images(c) as a functionof φ0 and gx

the image withthe minimumbackgroundenergy is theone with theleast aliasing

Truong et al. (in press) Magn. Reson. Med.

The 2nd row of E contains the motion-induced phase term exp[–iφ(x0, y0)]

aliasedimages

unaliasedimage

point spreadfunction

shot

1sh

ot 2

k-spacetrajectory

motion-induced

phase error

= ×a1

a2

u1

un

…

uN

…

2

P11

P21

P1N

P2N2

2

…

…

e–iφ e–iφEq. [1]

unknownknown

(N–x0+1:2N–x0,N–y0+1:2N–y0)

CPR for Two-Shot DW Spiral Imaging

φ is assumed to be spatially linear:φ(x, y) = φ0 + x gx + y gy

which is sufficient to correct forrigid-body motion*

A series of images are reconstructedby solving Eq. [1] with different φ0,gx , and gy values

The final image is chosen as the onewith the lowest signal intensity inthe background, i.e., with the leastamount of aliasing

…

…

φ0 / gx / gySba

ckgr

ound

min

*Anderson & Gore (1994) MRM 32: 379–87

CPR for Two-Shot DW Spiral Imaging

uncorrectedDWI images

correctedDWI images

uncorrectedADC maps

correctedADC maps

CPR Improves Diffusion Weighted Multi-Shot High-Resolution Spiral Imaging

Truong et al. (in press) Magn. Reson. Med.

CPR Improves Diffusion Weighted Multi-Shot EPI

Improvement in two-shot DW-EPI

After CorrectionAfter Correction

CPR Improves Four-Shot DW EPI

OriginalOriginalImagesImages

withwithReferenceReference

EchoesEchoes

OriginalOriginalImageImagewithwith

ReferenceReferenceEchoesEchoes

ImprovedImageafterCPR

Geometric Distortion is Another Major Challenge for High-Resolution DWI

128 echoes

160ms2.5 mm3

320mm

Distortion usually proportional to the readout window length

100ms2.5 mm3

320mm64 echoes

SENSE AccelerationFactor 2

EPI Distortions from Static Bo Inhomogeneity

DW EPI Distortions from Dynamic Eddy Current

DWDWEPIEPI

DWDWSpiralSpiral

Mapping Eddy Current Induced Field Changes

Truong et al., NeuroImage. 2011 Aug 15;57(4):1343-7

Field Map Based Distortion Correction

Truong et al., NeuroImage. 2011 Aug 15;57(4):1343-7

Field Map Based Deblurring in Spiral Imaging

[0.79, 0.32, 0.51] [‐0.66, 0.16, 0.72][0.00, 0.00, 0.00]

bobo DiffusionDiffusionDirection #1Direction #1

DiffusionDiffusionDirection #2Direction #2

Avram et al., ISMRM 2011

EchoEcho--shifting effect in EPIshifting effect in EPI

Can We Make Field Map Generation Inherent?

Chen et al., Neuroimage. 2006; 31(2):609-22Truong et al., Magn. Reson. Med. 2010; 64:1121-7

Inherent Field Mapping based on K-space Energy Spectrum Analysis (KESA)

Chen et al., Neuroimage. 2006; 31(2):609-22Truong et al., Magn. Reson. Med. 2010; 64:1121-7

Echo-Shifting Effect in DTI

Magnetic Field Maps in DTI

Summary

A practical yet powerful technical foundation for improved for improved DWI / DTI acquisition and reconstruction strategiesDWI / DTI acquisition and reconstruction strategies

Inherent correction for ghosting artifacts using cycling phase reconstruction (CPR) without the need for potentially without the need for potentially timetime--consuming reference echoes in highconsuming reference echoes in high--resolution DWIresolution DWI

Dynamic distortion correction based on inherently based on inherently generated field maps to restore spatial fidelitygenerated field maps to restore spatial fidelity

Generally applicable to all fast imaging techniques to all fast imaging techniques including EPI, Spiral, Propeller, and other kincluding EPI, Spiral, Propeller, and other k--space space trajectoriestrajectories

Nan-KueiChen

ChunleiLiu

AlexAvram

ArnaudGuidon

ToddHarshbarger

AnaBatrachenko

Trong-KhaTruong

NS 041328, EB 009483,NS 075017

Acknowledgement

Faculty and Staff at the Duke – UNC Brain Imaging and Analysis Center at Duke University www.biac.duke.eduFaculty and Staff at the Duke – UNC Brain Imaging and Analysis Center at Duke University www.biac.duke.edu

Documents

High Fidelity Brain Connectivity Imaging...Todd Harshbarger Ana Batrachenko Trong-Kha Truong NS 041328, EB 009483, NS 075017 Acknowledgement Faculty and Staff at the Duke – UNC Brain