XQ-SR: Joint x-q space super-resolution with application to infant diffusion MRI

Diffusion MRI (DMRI) is a powerful tool for studying early brain development and disorders. However, the typically low spatio-angular resolution of DMRI diminishes structural details and limits quantitative analysis to simple diffusion models. This problem is aggravated for infant DMRI since (i) the infant brain is significantly smaller than that of an adult, demanding higher spatial resolution to capture subtle structures; and (ii) the typically limited scan time of unsedated infants poses significant challenges to DMRI acquisition with high spatio-angular resolution. Post-acquisition super-resolution (SR) is an important alternative for increasing the resolution of DMRI data without prolonging acquisition times. However, most existing methods focus on the SR of only either the spatial domain (x-space) or the diffusion wavevector domain (q-space). For more effective resolution enhancement, we propose a framework for joint SR in both spatial and wavevector domains. More specifically, we first establish the signal relationships in x-q space using a robust neighborhood matching technique. We then harness the signal relationships to regularize the ill-posed inverse problem associated with the recovery of high-resolution data from their low-resolution counterpart. Extensive experiments on synthetic, adult, and infant DMRI data demonstrate that our method is able to recover high-resolution DMRI data with remarkably improved quality.

[1]  D. Tuch Q‐ball imaging , 2004, Magnetic resonance in medicine.

[2]  Weili Lin,et al.  Graph-Based Deep Learning for Prediction of Longitudinal Infant Diffusion MRI Data , 2019 .

[3]  Pew-Thian Yap,et al.  Longitudinal Prediction of Infant Diffusion MRI Data via Graph Convolutional Adversarial Networks , 2019, IEEE Transactions on Medical Imaging.

[4]  Tao Zhou,et al.  Multiview Latent Space Learning With Feature Redundancy Minimization , 2020, IEEE Transactions on Cybernetics.

[5]  Yue Cui,et al.  q-Space Learning with Synthesized Training Data , 2019, Computational Diffusion MRI.

[6]  Rebecca C. Knickmeyer,et al.  A Structural MRI Study of Human Brain Development from Birth to 2 Years , 2008, The Journal of Neuroscience.

[7]  Dorit Merhof,et al.  Direct Estimation of Fiber Orientations Using Deep Learning in Diffusion Imaging , 2016, MLMI@MICCAI.

[8]  Pew-Thian Yap,et al.  Reconstructing High-Quality Diffusion MRI Data from Orthogonal Slice-Undersampled Data Using Graph Convolutional Neural Networks , 2019, MICCAI.

[9]  Steen Moeller,et al.  The Human Connectome Project: A data acquisition perspective , 2012, NeuroImage.

[10]  Andrew L. Alexander,et al.  Diffusion tensor imaging of the corpus callosum in Autism , 2007, NeuroImage.

[11]  Dinggang Shen,et al.  Super-Resolution Reconstruction of Diffusion-Weighted Images using 4D Low-Rank and Total Variation , 2015, Computational diffusion MRI : MICCAI Workshop, Munich, Germany, October 9th, 2015. CDMRI (Workshop).

[12]  Bin Dong Sparse Representation on Graphs by Tight Wavelet Frames and Applications , 2014, 1411.2643.

[13]  Dinggang Shen,et al.  q-Space Upsampling Using x-q Space Regularization , 2017, MICCAI.

[14]  Dinggang Shen,et al.  Multi-Tissue Decomposition of Diffusion MRI Signals via $\ell _{0}$ Sparse-Group Estimation , 2016, IEEE Transactions on Image Processing.

[15]  Daniel Cremers,et al.  q-Space Deep Learning: Twelve-Fold Shorter and Model-Free Diffusion MRI Scans , 2016, IEEE Transactions on Medical Imaging.

[16]  F G Shellock,et al.  Auditory noise associated with MR procedures: a review. , 2000, Journal of magnetic resonance imaging : JMRI.

[17]  J. Gilmore,et al.  Mapping region-specific longitudinal cortical surface expansion from birth to 2 years of age. , 2013, Cerebral cortex.

[18]  Pew-Thian Yap,et al.  Robust Fusion of Diffusion MRI Data for Template Construction , 2017, Scientific Reports.

[19]  Michael Elad,et al.  Fast and robust multiframe super resolution , 2004, IEEE Transactions on Image Processing.

[20]  Chuyang Ye Estimation of Tissue Microstructure Using a Deep Network Inspired by a Sparse Reconstruction Framework , 2017, IPMI.

[21]  R. Deriche,et al.  Regularized, fast, and robust analytical Q‐ball imaging , 2007, Magnetic resonance in medicine.

[22]  D. Louis Collins,et al.  Non-local MRI upsampling , 2010, Medical Image Anal..

[23]  Chuyang Ye,et al.  A deep network for tissue microstructure estimation using modified LSTM units , 2019, Medical Image Anal..

[24]  G. Dehaene-Lambertz,et al.  The early development of brain white matter: A review of imaging studies in fetuses, newborns and infants , 2014, Neuroscience.

[25]  Karl Kunisch,et al.  Total Generalized Variation , 2010, SIAM J. Imaging Sci..

[26]  Wilson Fong Handbook of MRI Pulse Sequences , 2005 .

[27]  Dinggang Shen,et al.  Block-Based Statistics for Robust Non-parametric Morphometry , 2015, Patch-MI@MICCAI.

[28]  Carl-Fredrik Westin,et al.  A joint compressed-sensing and super-resolution approach for very high-resolution diffusion imaging , 2016, NeuroImage.

[29]  Jerry L. Prince,et al.  Fiber Orientation Estimation Guided by a Deep Network , 2017, MICCAI.

[30]  Antonio Criminisi,et al.  Image quality transfer and applications in diffusion MRI , 2017, NeuroImage.

[31]  J. Shewchuk An Introduction to the Conjugate Gradient Method Without the Agonizing Pain , 1994 .

[32]  Essa Yacoub,et al.  The WU-Minn Human Connectome Project: An overview , 2013, NeuroImage.

[33]  Mathews Jacob,et al.  Acceleration of high angular and spatial resolution diffusion imaging using compressed sensing with multichannel spiral data , 2015, Magnetic resonance in medicine.

[34]  Dinggang Shen,et al.  Spatio‐angular consistent construction of neonatal diffusion MRI atlases , 2017, Human brain mapping.

[35]  Dinggang Shen,et al.  Multifold Acceleration of Diffusion MRI via Deep Learning Reconstruction from Slice-Undersampled Data , 2019, IPMI.

[36]  Ke Li,et al.  Improving Estimation of Fiber Orientations in Diffusion MRI Using Inter-Subject Information Sharing , 2016, Scientific Reports.

[37]  Jean-Philippe Thiran,et al.  Phantomas: a flexible software library to simulate diffusion MR phantoms , 2014 .

[38]  Dinggang Shen,et al.  Tight Graph Framelets for Sparse Diffusion MRI q-Space Representation , 2016, MICCAI.

[39]  Jie Yang,et al.  Robust Visual Tracking via Online Discriminative and Low-Rank Dictionary Learning , 2018, IEEE Transactions on Cybernetics.

[40]  E. Bullmore,et al.  Formal characterization and extension of the linearized diffusion tensor model , 2005, Human brain mapping.

[41]  Michael Elad,et al.  Generalizing the Nonlocal-Means to Super-Resolution Reconstruction , 2009, IEEE Transactions on Image Processing.

[42]  Dinggang Shen,et al.  The UNC/UMN Baby Connectome Project (BCP): An overview of the study design and protocol development , 2019, NeuroImage.

[43]  Dinggang Shen,et al.  Joint 6D k-q Space Compressed Sensing for Accelerated High Angular Resolution Diffusion MRI , 2015, IPMI.

[44]  Dinggang Shen,et al.  Graph-Constrained Sparse Construction of Longitudinal Diffusion-Weighted Infant Atlases , 2017, MICCAI.

[45]  Dawn Fallik The Human Connectome Project Turns to Mapping Brain Development, from Birth through Early Childhood , 2016 .

[46]  Alan Connelly,et al.  Track-density imaging (TDI): Super-resolution white matter imaging using whole-brain track-density mapping , 2010, NeuroImage.

[47]  Daniel C. Alexander,et al.  Regularized super-resolution for diffusion MRI , 2008, 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro.

[48]  Antonio Criminisi,et al.  Bayesian Image Quality Transfer with CNNs: Exploring Uncertainty in dMRI Super-Resolution , 2017, MICCAI.

[49]  Jerry L. Prince,et al.  Estimation of fiber orientations using neighborhood information , 2016, Medical Image Anal..

[50]  Cheng Guan Koay,et al.  A signal transformational framework for breaking the noise floor and its applications in MRI. , 2009, Journal of magnetic resonance.

[51]  Guido Gerig,et al.  Diffusion tensor imaging: Application to the study of the developing brain. , 2007, Journal of the American Academy of Child and Adolescent Psychiatry.