A computational diffusion MRI and parametric dictionary learning framework for modeling the diffusion signal and its features

In this work, we first propose an original and efficient computational framework to model continuous diffusion MRI (dMRI) signals and analytically recover important diffusion features such as the Ensemble Average Propagator (EAP) and the Orientation Distribution Function (ODF). Then, we develop an efficient parametric dictionary learning algorithm and exploit the sparse property of a well-designed dictionary to recover the diffusion signal and its features with a reduced number of measurements. The properties and potentials of the technique are demonstrated using various simulations on synthetic data and on human brain data acquired from 7T and 3T scanners. It is shown that the technique can clearly recover the dMRI signal and its features with a much better accuracy compared to state-of-the-art approaches, even with a small and reduced number of measurements. In particular, we can accurately recover the ODF in regions of multiple fiber crossing, which could open new perspectives for some dMRI applications such as fiber tractography.

[1]  P. Grenier,et al.  MR imaging of intravoxel incoherent motions: application to diffusion and perfusion in neurologic disorders. , 1986, Radiology.

[2]  Yogesh Rathi,et al.  On Approximation of Orientation Distributions by Means of Spherical Ridgelets , 2008, IEEE Transactions on Image Processing.

[3]  Daniel C. Alexander,et al.  NODDI: Practical in vivo neurite orientation dispersion and density imaging of the human brain , 2012, NeuroImage.

[4]  Rachid Deriche,et al.  Theoretical Analysis and Practical Insights on EAP Estimation via a Unified HARDI Framework , 2011 .

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

[6]  Rachid Deriche,et al.  Diffusion MRI signal reconstruction with continuity constraint and optimal regularization , 2012, Medical Image Anal..

[7]  A. Bruckstein,et al.  K-SVD : An Algorithm for Designing of Overcomplete Dictionaries for Sparse Representation , 2005 .

[8]  Rachel Ward,et al.  Compressed Sensing With Cross Validation , 2008, IEEE Transactions on Information Theory.

[9]  Rachid Deriche,et al.  Optimal Design of Multiple Q-shells experiments for Diffusion MRI , 2011 .

[10]  C. Hardy,et al.  Accelerated diffusion spectrum imaging in the human brain using compressed sensing , 2011, Magnetic resonance in medicine.

[11]  Peter Craven,et al.  Smoothing noisy data with spline functions , 1978 .

[12]  Carl-Fredrik Westin,et al.  Probabilistic ODF Estimation from Reduced HARDI Data with Sparse Regularization , 2011, MICCAI.

[13]  Maxime Descoteaux,et al.  Sparse DSI: Learning DSI Structure for Denoising and Fast Imaging , 2012, MICCAI.

[14]  Rachid Deriche,et al.  Impact of Radial and Angular Sampling on Multiple Shells Acquisition in Diffusion MRI , 2011, MICCAI.

[15]  Yogesh Rathi,et al.  Spatially Regularized Compressed Sensing for High Angular Resolution Diffusion Imaging , 2011, IEEE Transactions on Medical Imaging.

[16]  Rachid Deriche,et al.  Compressed Sensing for Accelerated EAP Recovery in Diffusion MRI , 2010, MICCAI 2010.

[17]  Rachid Deriche,et al.  Multiple q-shell diffusion propagator imaging , 2011, Medical Image Anal..

[18]  J. E. Tanner,et al.  Spin diffusion measurements : spin echoes in the presence of a time-dependent field gradient , 1965 .

[19]  G. Wahba Smoothing noisy data with spline functions , 1975 .

[20]  P. Basser,et al.  Estimation of the effective self-diffusion tensor from the NMR spin echo. , 1994, Journal of magnetic resonance. Series B.

[21]  I. S. Gradshteyn,et al.  Table of Integrals, Series, and Products , 1976 .

[22]  Rachid Deriche,et al.  Deterministic and Probabilistic Tractography Based on Complex Fibre Orientation Distributions , 2009, IEEE Transactions on Medical Imaging.

[23]  Rachid Deriche,et al.  Optimal real-time Q-ball imaging using regularized Kalman filtering with incremental orientation sets , 2009, Medical Image Anal..

[24]  I. M. Pyshik,et al.  Table of integrals, series, and products , 1965 .

[25]  Carl-Fredrik Westin,et al.  Sparse Multi-Shell Diffusion Imaging , 2011, MICCAI.

[26]  Rachid Deriche,et al.  Parametric Dictionary Learning in Diffusion MRI , 2012, ISBI 2012.

[27]  Alan Connelly,et al.  Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution , 2007, NeuroImage.

[28]  Daniel C. Alexander,et al.  Maximum Entropy Spherical Deconvolution for Diffusion MRI , 2005, IPMI.

[29]  P. Basser Diffusion MRI: From Quantitative Measurement to In vivo Neuroanatomy , 2009 .

[30]  Chun-Hung Yeh,et al.  Resolving crossing fibres using constrained spherical deconvolution: Validation using diffusion-weighted imaging phantom data , 2008, NeuroImage.

[31]  Wenxing Ye,et al.  An over-complete dictionary based regularized reconstruction of a field of ensemble average propagators , 2012, 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI).

[32]  Rachid Deriche,et al.  Diffusion and multiple orientations from 1.5 MR systems with limited gradient tables , 2012 .

[33]  G. Sapiro,et al.  Reconstruction of the orientation distribution function in single‐ and multiple‐shell q‐ball imaging within constant solid angle , 2010, Magnetic resonance in medicine.

[34]  Rachid Deriche,et al.  Continuous diffusion signal, EAP and ODF estimation via Compressive Sensing in diffusion MRI , 2013, Medical Image Anal..

[35]  Carl-Fredrik Westin,et al.  Estimation of fiber Orientation Probability Density Functions in High Angular Resolution Diffusion Imaging , 2009, NeuroImage.

[36]  Marc Teboulle,et al.  A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems , 2009, SIAM J. Imaging Sci..

[37]  Julien Cohen-Adad,et al.  Accelerated diffusion spectrum imaging with compressed sensing using adaptive dictionaries , 2012, MICCAI.

[38]  R. Tibshirani,et al.  Least angle regression , 2004, math/0406456.

[39]  P. Hagmann,et al.  Mapping complex tissue architecture with diffusion spectrum magnetic resonance imaging , 2005, Magnetic resonance in medicine.

[40]  Rachid Deriche,et al.  Parametric Dictionary Learning for Modeling EAP and ODF in Diffusion MRI , 2012, MICCAI.

[41]  R. Tibshirani Regression Shrinkage and Selection via the Lasso , 1996 .

[42]  Baba C. Vemuri,et al.  A novel tensor distribution model for the diffusion-weighted MR signal , 2007, NeuroImage.

[43]  P. Basser,et al.  Simple harmonic oscillator based reconstruction and estimation for three-dimensional q-space MRI , 2009 .

[44]  M. Elad,et al.  $rm K$-SVD: An Algorithm for Designing Overcomplete Dictionaries for Sparse Representation , 2006, IEEE Transactions on Signal Processing.

[45]  A. Anderson Measurement of fiber orientation distributions using high angular resolution diffusion imaging , 2005, Magnetic resonance in medicine.

[46]  Luc Brun,et al.  Efficient and robust computation of PDF features from diffusion MR signal , 2009, Medical Image Anal..

[47]  M. Hutchinson,et al.  Smoothing noisy data with spline functions , 1985 .

[48]  P. Basser,et al.  MR diffusion tensor spectroscopy and imaging. , 1994, Biophysical journal.

[49]  Rachid Deriche,et al.  Ensemble Average Propagator Reconstruction via Compressed Sensing: Discrete or Continuous Bases ? , 2012 .

[50]  M. Horsfield,et al.  Optimal strategies for measuring diffusion in anisotropic systems by magnetic resonance imaging , 1999, Magnetic resonance in medicine.

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

[52]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..