ADEPT: Accurate Diffusion Echo-Planar imaging with multi-contrast shoTs
Corresponding Author
Banafshe Shafieizargar
imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Correspondence
Banafshe Shafieizargar, imec-Vision Lab, Department of Physics, University of Antwerp, Universiteitsplein 1, D.N.103, 2610, Antwerp, Belgium.
Email: [email protected]
Search for more papers by this authorBen Jeurissen
imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorDirk H. J. Poot
Department of Radiology and Nuclear Medicine, Biomedical Imaging Group Rotterdam, Erasmus MC, Rotterdam, The Netherlands
Search for more papers by this authorStefan Klein
Department of Radiology and Nuclear Medicine, Biomedical Imaging Group Rotterdam, Erasmus MC, Rotterdam, The Netherlands
Search for more papers by this authorJohan Van Audekerke
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorMarleen Verhoye
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorArnold J. den Dekker
imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorJan Sijbers
imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorCorresponding Author
Banafshe Shafieizargar
imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Correspondence
Banafshe Shafieizargar, imec-Vision Lab, Department of Physics, University of Antwerp, Universiteitsplein 1, D.N.103, 2610, Antwerp, Belgium.
Email: [email protected]
Search for more papers by this authorBen Jeurissen
imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorDirk H. J. Poot
Department of Radiology and Nuclear Medicine, Biomedical Imaging Group Rotterdam, Erasmus MC, Rotterdam, The Netherlands
Search for more papers by this authorStefan Klein
Department of Radiology and Nuclear Medicine, Biomedical Imaging Group Rotterdam, Erasmus MC, Rotterdam, The Netherlands
Search for more papers by this authorJohan Van Audekerke
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorMarleen Verhoye
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorArnold J. den Dekker
imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorJan Sijbers
imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium
NEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
Search for more papers by this authorFunding information: Fonds Wetenschappelijk Onderzoek, Grant/Award Numbers: 12M3119N; G084217N; H2020 Marie Skłodowska-Curie Actions, Grant/Award Number: 764513
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Abstract
Purpose
To introduce a novel imaging and parameter estimation framework for accurate multi-shot diffusion MRI.
Theory and Methods
We propose a new framework called ADEPT (Accurate Diffusion Echo-Planar imaging with multi-contrast shoTs) that enables fast diffusion MRI by allowing diffusion contrast settings to change between shots in a multi-shot EPI acquisition (i.e., intra-scan modulation). The framework estimates diffusion parameter maps directly from the acquired intra-scan modulated k-space data, while simultaneously accounting for shot-to-shot phase inconsistencies. The performance of the estimation framework is evaluated using Monte Carlo simulation studies and in-vivo experiments and compared to that of reference methods that rely on parallel imaging for shot-to-shot phase correction.
Results
Simulation and real-data experiments show that ADEPT yields more accurate and more precise estimates of the diffusion metrics in multi-shot EPI data in comparison with the reference methods.
Conclusion
ADEPT allows fast multi-shot EPI diffusion MRI without significantly degrading the accuracy and precision of the estimated diffusion maps.
Supporting Information
| Filename | Description |
|---|---|
| MRM29398-sup-0001-AppendixS1.pdfapplication/unknown, 1.9 MB | Appendix S1. Supporting information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- 1Farzaneh F, Riederer SJ, Pelc NJ. Analysis of T2 limitations and off-resonance effects on spatial resolution and artifacts in echo-planar imaging. Magn Reson Med. 1990; 14: 123-139.
- 2Le Bihan D, Poupon C, Amadon A, Lethimonnier F. Artifacts and pitfalls in diffusion MRI. J Magn Reson Imaging. 2006; 24: 478-488.
- 3Mani M, Jacob M, Kelley D, Magnotta V. Multi-shot sensitivity-encoded diffusion data recovery using structured low-rank matrix completion (MUSSELS). Magn Reson Med. 2017; 78: 494-507.
- 4Skare S, Newbould RD, Clayton DB, Albers GW, Nagle S, Bammer R. Clinical multishot DW-EPI through parallel imaging with considerations of susceptibility, motion, and noise. Magn Reson Med. 2007; 57: 881-890.
- 5Butts K, Riederer SJ, Ehman RL, Thompson RM, Jack CR. Interleaved echo planar imaging on a standard MRI system. Magn Reson Med. 1994; 31: 67-72.
- 6Bammer R, Stollberger R, Augustin M, et al. Diffusion-weighted imaging with navigated interleaved echo-planar imaging and a conventional gradient system. Radiology. 1999; 211: 799-806.
- 7Anderson AW, Gore JC. Analysis and correction of motion artifacts in diffusion weighted imaging. Magn Reson Med. 1994; 32: 379-387.
- 8Miller KL, Pauly JM. Nonlinear phase correction for navigated diffusion imaging. Magn Reson Med. 2003; 50: 343-353.
- 9Ma X, Zhang Z, Dai E, Guo H. Improved multi-shot diffusion imaging using GRAPPA with a compact kernel. NeuroImage. 2016; 138: 88-99.
- 10Jeong HK, Gore JC, Anderson AW. High-resolution human diffusion tensor imaging using 2-D navigated multishot SENSE EPI at 7 T. Magn Reson Med. 2013; 69: 793-802.
- 11Pipe JG, Farthing VG, Forbes KP. Multishot diffusion-weighted FSE using PROPELLER MRI. Magn Reson Med. 2002; 47: 42-52.
- 12Wen Q, Kodiweera C, Dale BM, Shivraman G, Wu YC. Rotating single-shot acquisition (RoSA) with composite reconstruction for fast high-resolution diffusion imaging. Magn Reson Med. 2018; 79: 264-275.
- 13Nunes RG, Jezzard P, Behrens TEJ, Clare S. Self-navigated multishot echo-planar pulse sequence for high-resolution diffusion-weighted imaging. Magn Reson Med. 2005; 53: 1474-1478.
- 14Zaitsev M, Zilles K, Shah NJ. Shared k-space echo planar imaging with keyhole. Magn Reson Med. 2001; 45: 109-117.
- 15Liu C, Bammer R, Kim DH, Moseley ME. Self-navigated interleaved spiral (SNAILS): application to high-resolution diffusion tensor imaging. Magn Reson Med. 2004; 52: 1388-1396.
- 16Pruessmann KP, Weiger M, Scheidegger MB, Boesiger P. SENSE: sensitivity encoding for fast MRI. Magn Reson Med. 1999; 42: 952-962.
10.1002/(SICI)1522-2594(199911)42:5<952::AID-MRM16>3.0.CO;2-S CAS PubMed Web of Science® Google Scholar
- 17Griswold MA, Jakob PM, Heidemann RM, et al. Generalized autocalibrating partially parallel acquisitions (GRAPPA). Magn Reson Med. 2002; 47: 1202-1210.
- 18Chen NK, Guidon A, Chang HC, Song AW. A robust multi-shot scan strategy for high-resolution diffusion weighted MRI enabled by multiplexed sensitivity-encoding (MUSE). NeuroImage. 2013; 72: 41-47.
- 19Guhaniyogi S, Chu ML, Chang HC, Song AW, Chen NK. Motion immune diffusion imaging using augmented MUSE for high-resolution multi-shot EPI. Magn Reson Med. 2016; 75: 639-652.
- 20Bruce IP, Chang HC, Petty C, Chen NK, Song AW. 3D-MB-MUSE: a robust 3D multi-slab, multi-band and multi-shot reconstruction approach for ultrahigh resolution diffusion MRI. NeuroImage. 2017; 159: 46-56.
- 21Wen Q, Feng L, Zhou K, Wu YC. Rapid golden-angle diffusion-weighted propeller MRI for simultaneous assessment of ADC and IVIM. NeuroImage. 2020; 223:117327.
- 22Welsh CL, Dibella EV, Adluru G, Hsu EW. Model-based reconstruction of undersampled diffusion tensor k-space data. Magn Reson Med. 2013; 70: 429-440.
- 23Zhu Y, Peng X, Wu Y, et al. Direct diffusion tensor estimation using a model-based method with spatial and parametric constraints. Med Phys. 2017; 44: 570-580.
- 24Knoll F, Raya JG, Halloran RO, et al. A model-based reconstruction for undersampled radial spin-echo DTI with variational penalties on the diffusion tensor. NMR Biomed. 2015; 28: 353-366.
- 25Dong Z, Dai E, Wang F, et al. Model-based reconstruction for simultaneous multislice and parallel imaging accelerated multishot diffusion tensor imaging. Med Phys. 2018; 45: 3196-3204.
- 26Mani M, Magnotta VA, Jacob M. qModeL: a plug-and-play model-based reconstruction for highly accelerated multi-shot diffusion MRI using learned priors. Magn Reson Med. 2021; 86: 835-851.
- 27Shafieizargar B, Jeurissen B, Poot DHJ, den Dekker AJ, Sijbers J. Multi-contrast multi-shot EPI for accelerated diffusion MRI. Proceedings of the 43rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society; 2021: 3869-3872.
- 28Shafieizargar B, Jeurissen B, Poot DHJ, et al. Accelerated multi-shot diffusion weighted imaging with joint estimation of diffusion and phase parameters. European Society for Magnetic Resonance in Medicine and Biology. Magnetic Resonance Materials in Physics; Vol. 34, 2021: S51-S53
- 29O'Halloran RL, Holdsworth S, Aksoy M, Bammer R. Model for the correction of motion-induced phase errors in multishot diffusion-weighted-MRI of the head: are cardiac-motion-induced phase errors reproducible from beat-to-beat? Magn Reson Med. 2012; 68: 430-440.
- 30Rabanillo I, Sanz-Estébanez S, Aja-Fernández S, Hajnal J, Alberola-López C, Cordero-Grande L. Joint image reconstruction and phase corruption maps estimation in multi-shot echo planar imaging. Computational Diffusion MRI; 2019: 19-27.
- 31Beck A, Tetruashvili L. On the convergence of block coordinate descent type methods. SIAM J Optim. 2013; 23: 2037-2060.
- 32Pruessmann KP, Weiger M, Börnert P, Boesiger P. Advances in sensitivity encoding with arbitrary k-space trajectories. Magn Reson Med. 2001; 46: 638-651.
- 33 The Mathworks, Inc. MATLAB version 9.5.0.944444 (R2018b), 2018; Natick, MA.
- 34Steihaug T. The conjugate gradient method and trust regions in large scale optimization. SIAM J Numer Anal. 1983; 20: 626-637.
- 35Yuan Y. Conditions for convergence of trust region algorithms for nonsmooth optimization. Math Program. 1985; 31: 220-228.
- 36Coleman TF, Li Y. On the convergence of interior-reflective Newton methods for nonlinear minimization subject to bounds. Math Program. 1994; 67: 189-224.
- 37Tamir JI, Ong F, Cheng JY, Uecker M, Lustig M. Generalized magnetic resonance image reconstruction using the Berkeley advanced reconstruction toolbox. Proceedings of the ISMRM Workshop on Data Sampling and Image Reconstruction; 2016; Sedona, AZ.
- 38Uecker M, Lai P, Murphy M, et al. ESPIRiT–an eigenvalue approach to autocalibrating parallel MRI: where SENSE meets GRAPPA. Magn Reson Med. 2014; 71: 990-1001.
- 39Collier Q, Veraart J, Jeurissen B, et al. Diffusion kurtosis imaging with free water elimination: a Bayesian estimation approach. Magn Reson Med. 2018; 80: 802-813.
- 40Papadakis NG, Murrills CD, Hall LD, Huang CL, Adrian CT. Minimal gradient encoding for robust estimation of diffusion anisotropy. Magn Reson Imaging. 2000; 18: 671-679.
- 41Byanju R, Klein S, Cristobal-Huerta A, Hernandez Tamames JA, Poot DHJ. Study of key properties behind a good undersampling pattern for quantitative estimation of tissue parameters. Proceedings of the 27th Annual Meeting of ISMRM; 2019: 4540; Montreal, Canada.
- 42den Dekker AJ, Sijbers J. Data distributions in magnetic resonance images: a review. Phys Med. 2014; 30: 725-741.
- 43Aja-Fernández S, Pieciak T, Vegas-Sánchez-Ferrero G. Spatially variant noise estimation in MRI: a homomorphic approach. Med Image Anal. 2015; 20: 184-197.
- 44Sijbers J, Vanrumste B, Van Hoey G, et al. Automatic localization of EEG electrode markers within 3D MR data. Magn Reson Imaging. 2000; 18: 485-488.
- 45Cordero-Grande L, Christiaens D, Hutter J, Price AN, Hajnal JV. Complex diffusion-weighted image estimation via matrix recovery under general noise models. NeuroImage. 2019; 200: 391-404.
- 46Tournier JD, Smith R, Raffelt D, et al. MRtrix3: a fast, flexible and open software framework for medical image processing and visualisation. NeuroImage. 2019; 202:116137.
- 47van den Bos A. Parameter Estimation for Scientists and Engineers. John Wiley Sons, Inc; 2007: 1-273.
10.1002/9780470173862.ch1 Google Scholar
- 48Vasanawala SS, Alley MT, Hargreaves BA, Barth RA, Pauly JM, Lustig M. Improved pediatric MR imaging with compressed sensing. Radiology. 2010; 256: 607-616.
- 49Hu Z, Ma X, Truong T-K, Song AW, Guo H. Phase-updated regularized SENSE for navigator-free multishot diffusion imaging. Magn Reson Med. 2017; 78: 172-181.
- 50Giannelli M, Diciotti S, Tessa C, Mascalchi M. Effect of echo spacing and readout bandwidth on basic performances of EPI-fMRI acquisition sequences implemented on two 1.5 T MR scanner systems. Med Phys. 2010; 37: 303-310.
- 51Jensen J, Helpern J, Ramani A, Lu H, Kaczynski K. Diffusional kurtosis imaging: the quantification of non-Gaussian water diffusion by means of magnetic resonance imaging. Magn Reson Med. 2005; 53: 1432-1440.
- 52Wang X, Rosenzweig S, Scholand N, Holme HCM, Uecker M. Model-based reconstruction for simultaneous multi-slice mapping using single-shot inversion-recovery radial FLASH. Magn Reson Med. 2021; 85: 1258-1271.
- 53Mani M, Jacob M, McKinnon G, et al. SMS MUSSELS: a navigator-free reconstruction for simultaneous multi-slice-accelerated multi-shot diffusion weighted imaging. Magn Reson Med. 2020; 83: 154-169.
- 54Ramos-Llordén G, den Dekker AJ, Van Steenkiste G, et al. A unified maximum likelihood framework for simultaneous motion and estimation in quantitative MR mapping. IEEE Trans Med Imaging. 2017; 36: 433-446.
- 55Gudbjartsson H, Patz S. The Rician distribution of noisy MRI data. Magn Reson Med. 1995; 34: 910-914.
- 56Andersen AH. On the Rician distribution of noisy MRI data. Magn Reson Med. 1996; 36: 331-333.
