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Park Y, Lee MJ, Yoo S, Kim CY, Namgung JY, Park Y, Park H, Lee EC, Yoon YD, Paquola C, Bernhardt BC, Park BY. GAN-MAT: Generative adversarial network-based microstructural profile covariance analysis toolbox. Neuroimage 2024; 291:120595. [PMID: 38554782 DOI: 10.1016/j.neuroimage.2024.120595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Multimodal magnetic resonance imaging (MRI) provides complementary information for investigating brain structure and function; for example, an in vivo microstructure-sensitive proxy can be estimated using the ratio between T1- and T2-weighted structural MRI. However, acquiring multiple imaging modalities is challenging in patients with inattentive disorders. In this study, we proposed a comprehensive framework to provide multiple imaging features related to the brain microstructure using only T1-weighted MRI. Our toolbox consists of (i) synthesizing T2-weighted MRI from T1-weighted MRI using a conditional generative adversarial network; (ii) estimating microstructural features, including intracortical covariance and moment features of cortical layer-wise microstructural profiles; and (iii) generating a microstructural gradient, which is a low-dimensional representation of the intracortical microstructure profile. We trained and tested our toolbox using T1- and T2-weighted MRI scans of 1,104 healthy young adults obtained from the Human Connectome Project database. We found that the synthesized T2-weighted MRI was very similar to the actual image and that the synthesized data successfully reproduced the microstructural features. The toolbox was validated using an independent dataset containing healthy controls and patients with episodic migraine as well as the atypical developmental condition of autism spectrum disorder. Our toolbox may provide a new paradigm for analyzing multimodal structural MRI in the neuroscience community and is openly accessible at https://github.com/CAMIN-neuro/GAN-MAT.
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Affiliation(s)
- Yeongjun Park
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Mi Ji Lee
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | | | - Chae Yeon Kim
- Department of Data Science, Inha University, Incheon, South Korea
| | | | - Yunseo Park
- Department of Data Science, Inha University, Incheon, South Korea
| | - Hyunjin Park
- School of Electronic and Electrical Engineering, Sungkyunkwan University, Suwon, South Korea; Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea
| | | | | | - Casey Paquola
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Jülich, Germany
| | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Bo-Yong Park
- Department of Data Science, Inha University, Incheon, South Korea; Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea; Department of Statistics and Data Science, Inha University, Incheon, South Korea.
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Wall J, Xie H, Wang X. Temporal Interactions between Maintenance of Cerebral Cortex Thickness and Physical Activity from an Individual Person Micro-Longitudinal Perspective and Implications for Precision Medicine. J Pers Med 2024; 14:127. [PMID: 38392561 PMCID: PMC10890462 DOI: 10.3390/jpm14020127] [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: 11/28/2023] [Revised: 12/30/2023] [Accepted: 01/09/2024] [Indexed: 02/24/2024] Open
Abstract
Maintenance of brain structure is essential for neurocognitive health. Precision medicine has interests in understanding how maintenance of an individual person's brain, including cerebral cortical structure, interacts with lifestyle factors like physical activity. Cortical structure, including cortical thickness, has recognized relationships with physical activity, but concepts of these relationships come from group, not individual, focused findings. Whether or how group-focused concepts apply to an individual person is fundamental to precision medicine interests but remains unclear. This issue was studied in a healthy man using concurrent micro-longitudinal tracking of magnetic resonance imaging-defined cortical thickness and accelerometer-defined steps/day over six months. These data permitted detailed examination of temporal relationships between thickness maintenance and physical activity at an individual level. Regression analyses revealed graded significant and trend-level temporal interactions between preceding activity vs. subsequent thickness maintenance and between preceding thickness maintenance vs. subsequent activity. Interactions were bidirectional, delayed/prolonged over days/weeks, positive, bilateral, directionally asymmetric, and limited in strength. These novel individual-focused findings in some ways are predicted, but in other ways remain unaddressed or undetected, by group-focused work. We suggest that individual-focused concepts of temporal interactions between maintenance of cortical structure and activity can provide needed new insight for personalized tailoring of physical activity, cortical, and neurocognitive health.
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Affiliation(s)
- John Wall
- Department of Neurosciences, University of Toledo College of Medicine & Life Sciences, Toledo, OH 43614, USA
| | - Hong Xie
- Department of Neurosciences, University of Toledo College of Medicine & Life Sciences, Toledo, OH 43614, USA
| | - Xin Wang
- Department of Neurosciences, University of Toledo College of Medicine & Life Sciences, Toledo, OH 43614, USA
- Department of Psychiatry, University of Toledo College of Medicine & Life Sciences, Toledo, OH 43614, USA
- Department of Radiology, University of Toledo College of Medicine & Life Sciences, Toledo, OH 43614, USA
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Chauvin L, Kumar K, Desrosiers C, Wells W, Toews M. Efficient Pairwise Neuroimage Analysis Using the Soft Jaccard Index and 3D Keypoint Sets. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:836-845. [PMID: 34699353 PMCID: PMC9022638 DOI: 10.1109/tmi.2021.3123252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We propose a novel pairwise distance measure between image keypoint sets, for the purpose of large-scale medical image indexing. Our measure generalizes the Jaccard index to account for soft set equivalence (SSE) between keypoint elements, via an adaptive kernel framework modeling uncertainty in keypoint appearance and geometry. A new kernel is proposed to quantify the variability of keypoint geometry in location and scale. Our distance measure may be estimated between O (N 2) image pairs in [Formula: see text] operations via keypoint indexing. Experiments report the first results for the task of predicting family relationships from medical images, using 1010 T1-weighted MRI brain volumes of 434 families including monozygotic and dizygotic twins, siblings and half-siblings sharing 100%-25% of their polymorphic genes. Soft set equivalence and the keypoint geometry kernel improve upon standard hard set equivalence (HSE) and appearance kernels alone in predicting family relationships. Monozygotic twin identification is near 100%, and three subjects with uncertain genotyping are automatically paired with their self-reported families, the first reported practical application of image-based family identification. Our distance measure can also be used to predict group categories, sex is predicted with an AUC = 0.97. Software is provided for efficient fine-grained curation of large, generic image datasets.
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Leong TKM, Lo WS, Lee WEZ, Tan B, Lee XZ, Lee LWJN, Lee JYJ, Suresh N, Loo LH, Szu E, Yeong J. Leveraging advances in immunopathology and artificial intelligence to analyze in vitro tumor models in composition and space. Adv Drug Deliv Rev 2021; 177:113959. [PMID: 34481035 DOI: 10.1016/j.addr.2021.113959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/17/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Cancer is the leading cause of death worldwide. Unfortunately, efforts to understand this disease are confounded by the complex, heterogenous tumor microenvironment (TME). Better understanding of the TME could lead to novel diagnostic, prognostic, and therapeutic discoveries. One way to achieve this involves in vitro tumor models that recapitulate the in vivo TME composition and spatial arrangement. Here, we review the potential of harnessing in vitro tumor models and artificial intelligence to delineate the TME. This includes (i) identification of novel features, (ii) investigation of higher-order relationships, and (iii) analysis and interpretation of multiomics data in a (iv) holistic, objective, reproducible, and efficient manner, which surpasses previous methods of TME analysis. We also discuss limitations of this approach, namely inadequate datasets, indeterminate biological correlations, ethical concerns, and logistical constraints; finally, we speculate on future avenues of research that could overcome these limitations, ultimately translating to improved clinical outcomes.
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Finn ES, Rosenberg MD. Beyond fingerprinting: Choosing predictive connectomes over reliable connectomes. Neuroimage 2021; 239:118254. [PMID: 34118397 DOI: 10.1016/j.neuroimage.2021.118254] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/25/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022] Open
Abstract
Recent years have seen a surge of research on variability in functional brain connectivity within and between individuals, with encouraging progress toward understanding the consequences of this variability for cognition and behavior. At the same time, well-founded concerns over rigor and reproducibility in psychology and neuroscience have led many to question whether functional connectivity is sufficiently reliable, and call for methods to improve its reliability. The thesis of this opinion piece is that when studying variability in functional connectivity-both across individuals and within individuals over time-we should use behavior prediction as our benchmark rather than optimize reliability for its own sake. We discuss theoretical and empirical evidence to compel this perspective, both when the goal is to study stable, trait-level differences between people, as well as when the goal is to study state-related changes within individuals. We hope that this piece will be useful to the neuroimaging community as we continue efforts to characterize inter- and intra-subject variability in brain function and build predictive models with an eye toward eventual real-world applications.
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Affiliation(s)
- Emily S Finn
- Department of Psychological and Brain Sciences, Dartmouth College, United States.
| | - Monica D Rosenberg
- Department of Psychology, University of Chicago, United States; Neuroscience Institute, University of Chicago, United States.
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