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Proceedings Paper

Deep learning estimation of multi-tissue constrained spherical deconvolution with limited single shell DW-MRI
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Paper Abstract

Diffusion-weighted magnetic resonance imaging (DW-MRI) is the only non-invasive approach for estimation of intravoxel tissue microarchitecture and reconstruction of in vivo neural pathways for the human brain. With improvement in accelerated MRI acquisition technologies, DW-MRI protocols that make use of multiple levels of diffusion sensitization have gained popularity. A well-known advanced method for reconstruction of white matter microstructure that uses multishell data is multi-tissue constrained spherical deconvolution (MT-CSD). MT-CSD substantially improves the resolution of intra-voxel structure over the traditional single shell version, constrained spherical deconvolution (CSD). Herein, we explore the possibility of using deep learning on single shell data (using the b=1000 s/mm2 from the Human Connectome Project (HCP)) to estimate the information content captured by 8th order MT-CSD using the full three shell data (b=1000, 2000, and 3000 s/mm2 from HCP). Briefly, we examine two network architectures: 1.) Sequential network of fully connected dense layers with a residual block in the middle (ResDNN), 2.) Patch based convolutional neural network with a residual block (ResCNN). For both networks an additional output block for estimation of voxel fraction was used with a modified loss function. Each approach was compared against the baseline of using MT-CSD on all data on 15 subjects from the HCP divided into 5 training, 2 validation, and 8 testing subjects with a total of 6.7 million voxels. The fiber orientation distribution function (fODF) can be recovered with high correlation (0.77 vs 0.74 and 0.65) and low root mean squared error ResCNN:0.0124, ResDNN:0.0168 and sCSD:0.0323 as compared to the ground truth of MT-CST, which was derived from the multi-shell DW-MRI acquisitions. The mean squared error between the MT-CSD estimates for white matter tissue fraction and for the predictions are ResCNN:0.0249 vs ResDNN:0.0264. We illustrate the applicability of high definition fiber tractography on a single testing subject with arcuate and corpus callosum Tractography. In summary, the proposed approach provides a promising framework to estimate MT-CSD with limited single shell data. Source code and models have been made publicly available.

Paper Details

Date Published: 10 March 2020
PDF: 10 pages
Proc. SPIE 11313, Medical Imaging 2020: Image Processing, 113130S (10 March 2020); doi: 10.1117/12.2549455
Show Author Affiliations
Vishwesh Nath, Vanderbilt Univ. (United States)
Sudhir K. Pathak, Univ. of Pittsburgh (United States)
Kurt G. Schilling, Vanderbilt Univ. Medical Ctr. (United States)
Walt Schneider, Univ. of Pittsburgh (United States)
Bennett A. Landman, Vanderbilt Univ. (United States)
Vanderbilt Univ. Medical Ctr. (United States)


Published in SPIE Proceedings Vol. 11313:
Medical Imaging 2020: Image Processing
Ivana Išgum; Bennett A. Landman, Editor(s)

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