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Warren SL, Khan DM, Moustafa AA. Assistive tools for classifying neurological disorders using fMRI and deep learning: A guide and example. Brain Behav 2024; 14:e3554. [PMID: 38841732 PMCID: PMC11154821 DOI: 10.1002/brb3.3554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Deep-learning (DL) methods are rapidly changing the way researchers classify neurological disorders. For example, combining functional magnetic resonance imaging (fMRI) and DL has helped researchers identify functional biomarkers of neurological disorders (e.g., brain activation and connectivity) and pilot innovative diagnostic models. However, the knowledge required to perform DL analyses is often domain-specific and is not widely taught in the brain sciences (e.g., psychology, neuroscience, and cognitive science). Conversely, neurological diagnoses and neuroimaging training (e.g., fMRI) are largely restricted to the brain and medical sciences. In turn, these disciplinary knowledge barriers and distinct specializations can act as hurdles that prevent the combination of fMRI and DL pipelines. The complexity of fMRI and DL methods also hinders their clinical adoption and generalization to real-world diagnoses. For example, most current models are not designed for clinical settings or use by nonspecialized populations such as students, clinicians, and healthcare workers. Accordingly, there is a growing area of assistive tools (e.g., software and programming packages) that aim to streamline and increase the accessibility of fMRI and DL pipelines for the diagnoses of neurological disorders. OBJECTIVES AND METHODS In this study, we present an introductory guide to some popular DL and fMRI assistive tools. We also create an example autism spectrum disorder (ASD) classification model using assistive tools (e.g., Optuna, GIFT, and the ABIDE preprocessed repository), fMRI, and a convolutional neural network. RESULTS In turn, we provide researchers with a guide to assistive tools and give an example of a streamlined fMRI and DL pipeline. CONCLUSIONS We are confident that this study can help more researchers enter the field and create accessible fMRI and deep-learning diagnostic models for neurological disorders.
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Affiliation(s)
- Samuel L. Warren
- Faculty of Society and Design, School of PsychologyBond UniversityGold CoastQueenslandAustralia
| | - Danish M. Khan
- Department of Electronic EngineeringNED University of Engineering & TechnologyKarachiSindhPakistan
| | - Ahmed A. Moustafa
- Faculty of Society and Design, School of PsychologyBond UniversityGold CoastQueenslandAustralia
- The Faculty of Health Sciences, Department of Human Anatomy and PhysiologyUniversity of JohannesburgAuckland ParkSouth Africa
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Xiao Z, He L, Zhao B, Jiang M, Mao W, Chen Y, Zhang T, Hu X, Liu T, Jiang X. Regularity and variability of functional brain connectivity characteristics between gyri and sulci under naturalistic stimulus. Comput Biol Med 2024; 168:107747. [PMID: 38039888 DOI: 10.1016/j.compbiomed.2023.107747] [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: 08/07/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023]
Abstract
The human cerebral cortex is folded into two fundamentally anatomical units: gyri and sulci. Previous studies have demonstrated the genetical, structural, and functional differences between gyri and sulci, providing a unique perspective for revealing the relationship among brain function, cognition, and behavior. While previous studies mainly focus on the functional differences between gyri and sulci under resting or task-evoked state, such characteristics under naturalistic stimulus (NS) which reflects real-world dynamic environments are largely unknown. To address this question, this study systematically investigates spatio-temporal functional connectivity (FC) characteristics between gyri and sulci under NS using a spatio-temporal graph convolutional network model. Based on the public Human Connectome Project dataset of 174 subjects with four different runs of both movie-watching NS and resting state 7T functional MRI data, we successfully identify unique FC features under NS, which are mainly involved in visual, auditory, emotional and cognitive control, and achieve high discriminative accuracy 93.06 % to resting state. Moreover, gyral regions as well as gyro-gyral connections consistently participate more as functional information exchange hubs than sulcal ones among these networks. This study provides novel insights into the functional brain mechanism under NS and lays a solid foundation for accurately mapping the brain anatomy-function relationship.
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Affiliation(s)
- Zhenxiang Xiao
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for NeuroInformation, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, Sichuan, China
| | - Liang He
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for NeuroInformation, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, Sichuan, China
| | - Boyu Zhao
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for NeuroInformation, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, Sichuan, China
| | - Mingxin Jiang
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for NeuroInformation, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, Sichuan, China
| | - Wei Mao
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for NeuroInformation, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, Sichuan, China
| | - Yuzhong Chen
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for NeuroInformation, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, Sichuan, China
| | - Tuo Zhang
- School of Automation, Northwestern Polytechnical University, 710129, Xi'an, China
| | - Xintao Hu
- School of Automation, Northwestern Polytechnical University, 710129, Xi'an, China
| | - Tianming Liu
- School of Computing, University of Georgia, 30602, Athens, USA
| | - Xi Jiang
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for NeuroInformation, School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, Sichuan, China.
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Amalric M, Cantlon JF. Entropy, complexity, and maturity in children’s neural responses to naturalistic video lessons. Cortex 2023; 163:14-25. [PMID: 37037065 DOI: 10.1016/j.cortex.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 11/29/2022] [Accepted: 02/17/2023] [Indexed: 03/19/2023]
Abstract
Temporal characteristics of neural signals are often overlooked in traditional fMRI developmental studies but are critical to studying brain functions in ecologically valid settings. In the present study, we explore the temporal properties of children's neural responses during naturalistic mathematics and grammar tasks. To do so, we introduce a novel measure in developmental fMRI: neural entropy, which indicates temporal complexity of BOLD signals. We show that temporal patterns of neural activity have lower complexity and greater variability in children than in adults in the association cortex but not in the sensory-motor cortex. We also show that neural entropy is associated with both child-adult similarity in functional connectivity and neural synchrony, and that neural entropy increases with the size of functionally connected networks in the association cortex. In addition, neural entropy increases with functional maturity (i.e., child-adult neural synchrony) in content-specific regions. These exploratory findings suggest the hypothesis that neural entropy indexes the increasing breadth and diversity of neural processes available to children for analyzing mathematical information over development.
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Affiliation(s)
- Marie Amalric
- Carnegie Mellon University, Department of Psychology, CAOs Laboratory, USA.
| | - Jessica F Cantlon
- Carnegie Mellon University, Department of Psychology, CAOs Laboratory, USA
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Campbell OL, Weber AM. Monofractal analysis of functional magnetic resonance imaging: An introductory review. Hum Brain Mapp 2022; 43:2693-2706. [PMID: 35266236 PMCID: PMC9057087 DOI: 10.1002/hbm.25801] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/11/2022] Open
Abstract
The following review will aid readers in providing an overview of scale-free dynamics and monofractal analysis, as well as its applications and potential in functional magnetic resonance imaging (fMRI) neuroscience and clinical research. Like natural phenomena such as the growth of a tree or crashing ocean waves, the brain expresses scale-invariant, or fractal, patterns in neural signals that can be measured. While neural phenomena may represent both monofractal and multifractal processes and can be quantified with many different interrelated parameters, this review will focus on monofractal analysis using the Hurst exponent (H). Monofractal analysis of fMRI data is an advanced analysis technique that measures the complexity of brain signaling by quantifying its degree of scale-invariance. As such, the H value of the blood oxygenation level-dependent (BOLD) signal specifies how the degree of correlation in the signal may mediate brain functions. This review presents a brief overview of the theory of fMRI monofractal analysis followed by notable findings in the field. Through highlighting the advantages and challenges of the technique, the article provides insight into how to best conduct fMRI fractal analysis and properly interpret the findings with physiological relevance. Furthermore, we identify the future directions necessary for its progression towards impactful functional neuroscience discoveries and widespread clinical use. Ultimately, this presenting review aims to build a foundation of knowledge among readers to facilitate greater understanding, discussion, and use of this unique yet powerful imaging analysis technique.
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Affiliation(s)
- Olivia Lauren Campbell
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Mark Weber
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Neuroscience, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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