Dr. Walter Schneider Profile

Dr. Walter Schneider

at Learning Research and Development Ctr.

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Publications (1)

Proceedings Article | 10 March 2020 Presentation + Paper

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

Vishwesh Nath, Sudhir Pathak, Kurt Schilling, Walt Schneider, Bennett Landman

Proceedings Volume 11313, 113130S (2020) https://doi.org/10.1117/12.2549455

KEYWORDS: Tissues, Medical research, Brain, Network architectures, Deconvolution, Magnetic resonance imaging, Diffusion, Diffusion tensor imaging, In vivo imaging

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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 8^th 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.

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