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Yao T, Rheault F, Cai LY, Nath V, Asad Z, Newlin N, Cui C, Deng R, Ramadass K, Shafer A, Resnick S, Schilling K, Landman BA, Huo Y. Robust fiber orientation distribution function estimation using deep constrained spherical deconvolution for diffusion-weighted magnetic resonance imaging. J Med Imaging (Bellingham) 2024; 11:014005. [PMID: 38188934 PMCID: PMC10768686 DOI: 10.1117/1.jmi.11.1.014005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/04/2023] [Accepted: 12/14/2023] [Indexed: 01/09/2024] Open
Abstract
Purpose Diffusion-weighted magnetic resonance imaging (DW-MRI) is a critical imaging method for capturing and modeling tissue microarchitecture at a millimeter scale. A common practice to model the measured DW-MRI signal is via fiber orientation distribution function (fODF). This function is the essential first step for the downstream tractography and connectivity analyses. With recent advantages in data sharing, large-scale multisite DW-MRI datasets are being made available for multisite studies. However, measurement variabilities (e.g., inter- and intrasite variability, hardware performance, and sequence design) are inevitable during the acquisition of DW-MRI. Most existing model-based methods [e.g., constrained spherical deconvolution (CSD)] and learning-based methods (e.g., deep learning) do not explicitly consider such variabilities in fODF modeling, which consequently leads to inferior performance on multisite and/or longitudinal diffusion studies. Approach In this paper, we propose a data-driven deep CSD method to explicitly constrain the scan-rescan variabilities for a more reproducible and robust estimation of brain microstructure from repeated DW-MRI scans. Specifically, the proposed method introduces a three-dimensional volumetric scanner-invariant regularization scheme during the fODF estimation. We study the Human Connectome Project (HCP) young adults test-retest group as well as the MASiVar dataset (with inter- and intrasite scan/rescan data). The Baltimore Longitudinal Study of Aging dataset is employed for external validation. Results From the experimental results, the proposed data-driven framework outperforms the existing benchmarks in repeated fODF estimation. By introducing the contrastive loss with scan/rescan data, the proposed method achieved a higher consistency while maintaining higher angular correlation coefficients with the CSD modeling. The proposed method is assessing the downstream connectivity analysis and shows increased performance in distinguishing subjects with different biomarkers. Conclusion We propose a deep CSD method to explicitly reduce the scan-rescan variabilities, so as to model a more reproducible and robust brain microstructure from repeated DW-MRI scans. The plug-and-play design of the proposed approach is potentially applicable to a wider range of data harmonization problems in neuroimaging.
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Affiliation(s)
- Tianyuan Yao
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Francois Rheault
- Université de Sherbrooke, Department of Computer Science, Sherbrooke, Québec, Canada
| | - Leon Y. Cai
- Vanderbilt University, Department of Biomedical Engineering, Nashville, Tennessee, United States
| | - Vishwesh Nath
- NVIDIA Corporation, Bethesda, Maryland, United States
| | - Zuhayr Asad
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Nancy Newlin
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Can Cui
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Ruining Deng
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Karthik Ramadass
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Andrea Shafer
- National Institute on Aging, Laboratory of Behavioral Neuroscience, Baltimore, Maryland, United States
| | - Susan Resnick
- National Institute on Aging, Laboratory of Behavioral Neuroscience, Baltimore, Maryland, United States
| | - Kurt Schilling
- Vanderbilt University, Department of Biomedical Engineering, Nashville, Tennessee, United States
| | - Bennett A. Landman
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
- Vanderbilt University, Department of Biomedical Engineering, Nashville, Tennessee, United States
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, Tennessee, United States
| | - Yuankai Huo
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, Tennessee, United States
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Radhakrishnan H, Shabestari SK, Blurton-Jones M, Obenaus A, Stark CEL. Using Advanced Diffusion-Weighted Imaging to Predict Cell Counts in Gray Matter: Potential and Pitfalls. Front Neurosci 2022; 16:881713. [PMID: 35720733 PMCID: PMC9204138 DOI: 10.3389/fnins.2022.881713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/18/2022] [Indexed: 11/22/2022] Open
Abstract
Recent advances in diffusion imaging have given it the potential to non-invasively detect explicit neurobiological properties, beyond what was previously possible with conventional structural imaging. However, there is very little known about what cytoarchitectural properties these metrics, especially those derived from newer multi-shell models like Neurite Orientation Dispersion and Density Imaging (NODDI) correspond to. While these diffusion metrics do not promise any inherent cell type specificity, different brain cells have varying morphologies, which could influence the diffusion signal in distinct ways. This relationship is currently not well-characterized. Understanding the possible cytoarchitectural signatures of diffusion measures could allow them to estimate important neurobiological properties like cell counts, potentially resulting in a powerful clinical diagnostic tool. Here, using advanced diffusion imaging (NODDI) in the mouse brain, we demonstrate that different regions have unique relationships between cell counts and diffusion metrics. We take advantage of this exclusivity to introduce a framework to predict cell counts of different types of cells from the diffusion metrics alone, in a region-specific manner. We also outline the challenges of reliably developing such a model and discuss the precautions the field must take when trying to tie together medical imaging modalities and histology.
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Affiliation(s)
- Hamsanandini Radhakrishnan
- Mathematical, Computational and Systems Biology, University of California, Irvine, Irvine, CA, United States
| | - Sepideh Kiani Shabestari
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Mathew Blurton-Jones
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Andre Obenaus
- Department of Pediatrics, School of Medicine, University of California, Irvine, Irvine, CA, United States
| | - Craig E. L. Stark
- Mathematical, Computational and Systems Biology, University of California, Irvine, Irvine, CA, United States
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
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Zhang F, Wells WM, O'Donnell LJ. Deep Diffusion MRI Registration (DDMReg): A Deep Learning Method for Diffusion MRI Registration. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:1454-1467. [PMID: 34968177 PMCID: PMC9273049 DOI: 10.1109/tmi.2021.3139507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this paper, we present a deep learning method, DDMReg, for accurate registration between diffusion MRI (dMRI) datasets. In dMRI registration, the goal is to spatially align brain anatomical structures while ensuring that local fiber orientations remain consistent with the underlying white matter fiber tract anatomy. DDMReg is a novel method that uses joint whole-brain and tract-specific information for dMRI registration. Based on the successful VoxelMorph framework for image registration, we propose a novel registration architecture that leverages not only whole brain information but also tract-specific fiber orientation information. DDMReg is an unsupervised method for deformable registration between pairs of dMRI datasets: it does not require nonlinearly pre-registered training data or the corresponding deformation fields as ground truth. We perform comparisons with four state-of-the-art registration methods on multiple independently acquired datasets from different populations (including teenagers, young and elderly adults) and different imaging protocols and scanners. We evaluate the registration performance by assessing the ability to align anatomically corresponding brain structures and ensure fiber spatial agreement between different subjects after registration. Experimental results show that DDMReg obtains significantly improved registration performance compared to the state-of-the-art methods. Importantly, we demonstrate successful generalization of DDMReg to dMRI data from different populations with varying ages and acquired using different acquisition protocols and different scanners.
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Liu Z, Moon HS, Li Z, Laforest R, Perlmutter JS, Norris SA, Jha AK. A tissue‐fraction estimation‐based segmentation method for quantitative dopamine transporter SPECT. Med Phys 2022; 49:5121-5137. [PMID: 35635327 PMCID: PMC9703616 DOI: 10.1002/mp.15778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/25/2022] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Quantitative measures of dopamine transporter (DaT) uptake in caudate, putamen, and globus pallidus (GP) derived from dopamine transporter-single-photon emission computed tomography (DaT-SPECT) images have potential as biomarkers for measuring the severity of Parkinson's disease. Reliable quantification of this uptake requires accurate segmentation of the considered regions. However, segmentation of these regions from DaT-SPECT images is challenging, a major reason being partial-volume effects (PVEs) in SPECT. The PVEs arise from two sources, namely the limited system resolution and reconstruction of images over finite-sized voxel grids. The limited system resolution results in blurred boundaries of the different regions. The finite voxel size leads to TFEs, that is, voxels contain a mixture of regions. Thus, there is an important need for methods that can account for the PVEs, including the TFEs, and accurately segment the caudate, putamen, and GP, from DaT-SPECT images. PURPOSE Design and objectively evaluate a fully automated tissue-fraction estimation-based segmentation method that segments the caudate, putamen, and GP from DaT-SPECT images. METHODS The proposed method estimates the posterior mean of the fractional volumes occupied by the caudate, putamen, and GP within each voxel of a three-dimensional DaT-SPECT image. The estimate is obtained by minimizing a cost function based on the binary cross-entropy loss between the true and estimated fractional volumes over a population of SPECT images, where the distribution of true fractional volumes is obtained from existing populations of clinical magnetic resonance images. The method is implemented using a supervised deep-learning-based approach. RESULTS Evaluations using clinically guided highly realistic simulation studies show that the proposed method accurately segmented the caudate, putamen, and GP with high mean Dice similarity coefficients of ∼ 0.80 and significantly outperformed ( p < 0.01 $p < 0.01$ ) all other considered segmentation methods. Further, an objective evaluation of the proposed method on the task of quantifying regional uptake shows that the method yielded reliable quantification with low ensemble normalized root mean square error (NRMSE) < 20% for all the considered regions. In particular, the method yielded an even lower ensemble NRMSE of ∼ 10% for the caudate and putamen. CONCLUSIONS The proposed tissue-fraction estimation-based segmentation method for DaT-SPECT images demonstrated the ability to accurately segment the caudate, putamen, and GP, and reliably quantify the uptake within these regions. The results motivate further evaluation of the method with physical-phantom and patient studies.
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Affiliation(s)
- Ziping Liu
- Department of Biomedical Engineering Washington University St. Louis MO 63130 United States of America
| | - Hae Sol Moon
- Department of Biomedical Engineering Washington University St. Louis MO 63130 United States of America
| | - Zekun Li
- Department of Biomedical Engineering Washington University St. Louis MO 63130 United States of America
| | - Richard Laforest
- Mallinckrodt Institute of Radiology Washington University School of Medicine St. Louis MO 63110 United States of America
| | - Joel S. Perlmutter
- Mallinckrodt Institute of Radiology Washington University School of Medicine St. Louis MO 63110 United States of America
- Department of Neurology Washington University School of Medicine St. Louis MO 63110 United States of America
| | - Scott A. Norris
- Mallinckrodt Institute of Radiology Washington University School of Medicine St. Louis MO 63110 United States of America
- Department of Neurology Washington University School of Medicine St. Louis MO 63110 United States of America
| | - Abhinav K. Jha
- Department of Biomedical Engineering Washington University St. Louis MO 63130 United States of America
- Mallinckrodt Institute of Radiology Washington University School of Medicine St. Louis MO 63110 United States of America
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Liu Z, Mhlanga JC, Laforest R, Derenoncourt PR, Siegel BA, Jha AK. A Bayesian approach to tissue-fraction estimation for oncological PET segmentation. Phys Med Biol 2021; 66. [PMID: 34125078 PMCID: PMC8765116 DOI: 10.1088/1361-6560/ac01f4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/17/2021] [Indexed: 01/06/2023]
Abstract
Tumor segmentation in oncological PET is challenging, a major reason being the partial-volume effects (PVEs) that arise due to low system resolution and finite voxel size. The latter results in tissue-fraction effects (TFEs), i.e. voxels contain a mixture of tissue classes. Conventional segmentation methods are typically designed to assign each image voxel as belonging to a certain tissue class. Thus, these methods are inherently limited in modeling TFEs. To address the challenge of accounting for PVEs, and in particular, TFEs, we propose a Bayesian approach to tissue-fraction estimation for oncological PET segmentation. Specifically, this Bayesian approach estimates the posterior mean of the fractional volume that the tumor occupies within each image voxel. The proposed method, implemented using a deep-learning-based technique, was first evaluated using clinically realistic 2D simulation studies with known ground truth, in the context of segmenting the primary tumor in PET images of patients with lung cancer. The evaluation studies demonstrated that the method accurately estimated the tumor-fraction areas and significantly outperformed widely used conventional PET segmentation methods, including a U-net-based method, on the task of segmenting the tumor. In addition, the proposed method was relatively insensitive to PVEs and yielded reliable tumor segmentation for different clinical-scanner configurations. The method was then evaluated using clinical images of patients with stage IIB/III non-small cell lung cancer from ACRIN 6668/RTOG 0235 multi-center clinical trial. Here, the results showed that the proposed method significantly outperformed all other considered methods and yielded accurate tumor segmentation on patient images with Dice similarity coefficient (DSC) of 0.82 (95% CI: 0.78, 0.86). In particular, the method accurately segmented relatively small tumors, yielding a high DSC of 0.77 for the smallest segmented cross-section of 1.30 cm2. Overall, this study demonstrates the efficacy of the proposed method to accurately segment tumors in PET images.
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Affiliation(s)
- Ziping Liu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, United States of America
| | - Joyce C Mhlanga
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Richard Laforest
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Paul-Robert Derenoncourt
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Barry A Siegel
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Abhinav K Jha
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, United States of America.,Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
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