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
2 mm into GM0diamagnetic paramagnetic
3 mm into GM0diamagnetic paramagnetic
4 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
Chen et al.,Magn Reson Med. 2011 Oct;66(4):1057-66
CPR for 2D EPI
Chen et al.,Magn Reson Med. 2011 Oct;66(4):1057-66
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