Magnetic Resonance Imaging Datasets Research Articles

Enhancing Brain Segmentation in MRI through Integration of Hidden Markov Random Field Model and Whale Optimization Algorithm

The automatic delineation and segmentation of the brain tissues from Magnetic Resonance Images (MRIs) is a great challenge in the medical context. The difficulty of this task arises out of the similar visual appearance of neighboring brain structures in MR images. In this study, we present an automatic approach for robust and accurate brain tissue boundary outlining in MR images. This algorithm is proposed for the tissue classification of MR brain images into White Matter (WM), Gray Matter (GM) and Cerebrospinal Fluid (CSF). The proposed segmentation process combines two algorithms, the Hidden Markov Random Field (HMRF) model and the Whale Optimization Algorithm (WOA), to enhance the treatment accuracy. In addition, we use the Whale Optimization Algorithm (WOA) to optimize the performance of the segmentation method. The experimental results from a dataset of brain MR images show the superiority of our proposed method, referred to HMRF-WOA, as compared to other reported approaches. The HMRF-WOA is evaluated on multiple MRI contrasts, including both simulated and real MR brain images. The well-known Dice coefficient (DC) and Jaccard coefficient (JC) were used as similarity metrics. The results show that, in many cases, our proposed method approaches the perfect segmentation with a Dice coefficient and Jaccard coefficient above 0.9.

A multi-institutional meningioma MRI dataset for automated multi-sequence image segmentation

Meningiomas are the most common primary intracranial tumors and can be associated with significant morbidity and mortality. Radiologists, neurosurgeons, neuro-oncologists, and radiation oncologists rely on brain MRI for diagnosis, treatment planning, and longitudinal treatment monitoring. However, automated, objective, and quantitative tools for non-invasive assessment of meningiomas on multi-sequence MR images are not available. Here we present the BraTS Pre-operative Meningioma Dataset, as the largest multi-institutional expert annotated multilabel meningioma multi-sequence MR image dataset to date. This dataset includes 1,141 multi-sequence MR images from six sites, each with four structural MRI sequences (T2-, T2/FLAIR-, pre-contrast T1-, and post-contrast T1-weighted) accompanied by expert manually refined segmentations of three distinct meningioma sub-compartments: enhancing tumor, non-enhancing tumor, and surrounding non-enhancing T2/FLAIR hyperintensity. Basic demographic data are provided including age at time of initial imaging, sex, and CNS WHO grade. The goal of releasing this dataset is to facilitate the development of automated computational methods for meningioma segmentation and expedite their incorporation into clinical practice, ultimately targeting improvement in the care of meningioma patients.

A novel approach of brain-computer interfacing (BCI) and Grad-CAM based explainable artificial intelligence: Use case scenario for smart healthcare

BackgroundIn order to push the frontiers of brain-computer interface (BCI) and neuron-electronics, this research presents a novel framework that combines cutting-edge technologies for improved brain-related diagnostics in smart healthcare. This research offers a ground-breaking application of transparent strategies to BCI, promoting openness and confidence in brain-computer interactions and taking inspiration from Grad-CAM (Gradient-weighted Class Activation Mapping) based Explainable Artificial Intelligence (XAI) methodology. The landscape of healthcare diagnostics is about to be redefined by the integration of various technologies, especially when it comes to illnesses related to the brain. New methodA novel approach has been proposed in this study comprising of Xception architecture which is trained on imagenet database following transfer learning process for extraction of significant features from magnetic resonance imaging dataset acquired from publicly available distinct sources as an input and linear support vector machine has been used for distinguishing distinct classes.Afterwards, gradient-weighted class activation mapping has been deployed as the foundation for explainable artificial intelligence (XAI) for generating informative heatmaps, representing spatial localization of features which were focused to achieve model’s predictions. ResultsThus, the proposed model not only provides accurate outcomes but also provides transparency for the predictions generated by the Xception network to diagnose presence of abnormal tissues and avoids overfitting issues. Hyperparameters along with performance-metrics are also obtained while validating the proposed network on unseen brain MRI scans to ensure effectiveness of the proposed network. Comparison with existing methods and conclusionsThe integration of Grad-CAM based explainable artificial intelligence with deep neural network namely Xception offers a significant impact in diagnosing brain tumor disease while highlighting the specific regions of input brain MRI images responsible for making predictions. In this study, the proposed network results in 98.92% accuracy, 98.15% precision, 99.09% sensitivity, 98.18% specificity and 98.91% dice-coefficient while identifying presence of abnormal tissues in the brain. Thus, Xception model trained on distinct dataset following transfer learning process offers remarkable diagnostic accuracy and linear support vector act as a classifier to provide efficient classification among distinct classes. In addition, the deployed explainable artificial intelligence approach helps in revealing the reasoning behind predictions made by deep neural network having black-box nature and provides a clear perspective to assist medical experts in achieving trustworthiness and transparency while diagnosing brain tumor disease in the smart healthcare

Towards a unified approach for unsupervised brain MRI Motion Artefact Detection with few shot Anomaly Detection

Automated Motion Artefact Detection (MAD) in Magnetic Resonance Imaging (MRI) is a field of study that aims to automatically flag motion artefacts in order to prevent the requirement for a repeat scan. In this paper, we identify and tackle the three current challenges in the field of automated MAD; (1) reliance on fully-supervised training, meaning they require specific examples of Motion Artefacts (MA), (2) inconsistent use of benchmark datasets across different works and use of private datasets for testing and training of newly proposed MAD techniques and (3) a lack of sufficiently large datasets for MRI MAD. To address these challenges, we demonstrate how MAs can be identified by formulating the problem as an unsupervised Anomaly Detection (AD) task. We compare the performance of three State-of-the-Art AD algorithms DeepSVDD, Interpolated Gaussian Descriptor and FewSOME on two open-source Brain MRI datasets on the task of MAD and MA severity classification, with FewSOME achieving a MAD AUC >90% on both datasets and a Spearman Rank Correlation Coefficient of 0.8 on the task of MA severity classification. These models are trained in the few shot setting, meaning large Brain MRI datasets are not required to build robust MAD algorithms. This work also sets a standard protocol for testing MAD algorithms on open-source benchmark datasets. In addition to addressing these challenges, we demonstrate how our proposed ‘anomaly-aware’ scoring function improves FewSOME’s MAD performance in the setting where one and two shots of the anomalous class are available for training. Code available at https://github.com/niamhbelton/Unsupervised-Brain-MRI-Motion-Artefact-Detection/.

Artificial intelligence for volumetric measurement of cerebral white matter hyperintensities on thick-slice fluid-attenuated inversion recovery (FLAIR) magnetic resonance images from multiple centers

We aimed to develop a new artificial intelligence software that can automatically extract and measure the volume of white matter hyperintensities (WMHs) in head magnetic resonance imaging (MRI) using only thick-slice fluid-attenuated inversion recovery (FLAIR) sequences from multiple centers. We enrolled 1092 participants in Japan, comprising the thick-slice Private Dataset. Based on 207 randomly selected participants, neuroradiologists annotated WMHs using predefined guidelines. The annotated images of participants were divided into training (n = 138) and test (n = 69) datasets. The WMH segmentation model comprised a U-Net ensemble and was trained using the Private Dataset. Two other models were trained for validation using either both thin- and thick-slice MRI datasets or the thin-slice dataset alone. The voxel-wise Dice similarity coefficient (DSC) was used as the evaluation metric. The model trained using only thick-slice MRI showed a DSC of 0.820 for the test dataset, which is comparable to the accuracy of human readers. The model trained with the additional thin-slice dataset showed only a slightly improved DSC of 0.822. This automatic WMH segmentation model comprising a U-Net ensemble trained on a thick-slice FLAIR MRI dataset is a promising new method. Despite some limitations, this model may be applicable in clinical practice.

Attentional adversarial training for few-shot medical image segmentation without annotations.

Medical image segmentation is a critical application that plays a significant role in clinical research. Despite the fact that many deep neural networks have achieved quite high accuracy in the field of medical image segmentation, there is still a scarcity of annotated labels, making it difficult to train a robust and generalized model. Few-shot learning has the potential to predict new classes that are unseen in training with a few annotations. In this study, a novel few-shot semantic segmentation framework named prototype-based generative adversarial network (PG-Net) is proposed for medical image segmentation without annotations. The proposed PG-Net consists of two subnetworks: the prototype-based segmentation network (P-Net) and the guided evaluation network (G-Net). On one hand, the P-Net as a generator focuses on extracting multi-scale features and local spatial information in order to produce refined predictions with discriminative context between foreground and background. On the other hand, the G-Net as a discriminator, which employs an attention mechanism, further distills the relation knowledge between support and query, and contributes to P-Net producing segmentation masks of query with more similar distributions as support. Hence, the PG-Net can enhance segmentation quality by an adversarial training strategy. Compared to the state-of-the-art (SOTA) few-shot segmentation methods, comparative experiments demonstrate that the proposed PG-Net provides noticeably more robust and prominent generalization ability on different medical image modality datasets, including an abdominal Computed Tomography (CT) dataset and an abdominal Magnetic Resonance Imaging (MRI) dataset.

Swin Transformer and the Unet Architecture to Correct Motion Artifacts in Magnetic Resonance Image Reconstruction.

We present a deep learning-based method that corrects motion artifacts and thus accelerates data acquisition and reconstruction of magnetic resonance images. The novel model, the Motion Artifact Correction by Swin Network (MACS-Net), uses a Swin transformer layer as the fundamental block and the Unet architecture as the neural network backbone. We employ a hierarchical transformer with shifted windows to extract multiscale contextual features during encoding. A new dual upsampling technique is employed to enhance the spatial resolutions of feature maps in the Swin transformer-based decoder layer. A raw magnetic resonance imaging dataset is used for network training and testing; the data contain various motion artifacts with ground truth images of the same subjects. The results were compared to six state-of-the-art MRI image motion correction methods using two types of motions. When motions were brief (within 5 s), the method reduced the average normalized root mean square error (NRMSE) from 45.25% to 17.51%, increased the mean structural similarity index measure (SSIM) from 79.43% to 91.72%, and increased the peak signal-to-noise ratio (PSNR) from 18.24 to 26.57 dB. Similarly, when motions were extended from 5 to 10 s, our approach decreased the average NRMSE from 60.30% to 21.04%, improved the mean SSIM from 33.86% to 90.33%, and increased the PSNR from 15.64 to 24.99 dB. The anatomical structures of the corrected images and the motion-free brain data were similar.

Functionality of arousal-regulating brain circuitry at rest predicts human cognitive abilities.

Arousal state is regulated by subcortical neuromodulatory nuclei, such as locus coeruleus, which send wide-reaching projections to cortex. Whether higher-order cortical regions have the capacity to recruit neuromodulatory systems to aid cognition is unclear. Here, we hypothesized that select cortical regions activate the arousal system, which, in turn, modulates large-scale brain activity, creating a functional circuit predicting cognitive ability. We utilized the Human Connectome Project 7T functional magnetic resonance imaging dataset (n = 149), acquired at rest with simultaneous eye tracking, along with extensive cognitive assessment for each subject. First, we discovered select frontoparietal cortical regions that drive large-scale spontaneous brain activity specifically via engaging the arousal system. Second, we show that the functionality of the arousal circuit driven by bilateral posterior cingulate cortex (associated with the default mode network) predicts subjects' cognitive abilities. This suggests that a cortical region that is typically associated with self-referential processing supports cognition by regulating the arousal system.

Bridging Modalities: A Multimodal Machine Learning Approach for Parkinson’s Disease Diagnosis Using EEG and MRI Data

Parkinson’s disease (PD) is a slowly progressing neurological disorder with symptoms that overlap with those of other conditions, making early detection and accurate diagnosis vital for effective treatment and a patient’s quality of life. Symptoms such as tremors, stiffness, slow movements, and balance issues, along with psychiatric manifestations, are typical of PD. This study introduces a groundbreaking approach to PD diagnosis, utilizing a multimodal machine learning framework that integrates Electroencephalography (EEG) and Magnetic Resonance Imaging (MRI) data. Focusing on the early detection and accurate classification of PD, the proposed research leverages the distinct yet complementary nature of EEG and MRI datasets to enhance diagnostic precision. We employed a robust algorithmic strategy, including LightGBM and machine learning techniques, to analyze the complex patterns inherent in neurological data. The key steps of the proposed research are preprocessing and feature extraction from both EEG and MRI modalities, followed by their fusion using Principal Component Analysis (PCA) for dimensionality reduction. The fused dataset was then analyzed using a LightGBM model and validated through a 10-fold cross-validation process to ensure reliability and stability. The model’s efficacy was further tested on independent datasets, demonstrating its robustness across diverse patient demographics. The obtained results showcased an accuracy of 97.17%, sensitivity of 96.58%, and specificity of 96.82% in PD classification, outperforming traditional multimodal as well as single-modality diagnostic methods. The integration of EEG and MRI data provided a more comprehensive view of the neurophysiological and neuroanatomical changes associated with PD. Additionally, the use of advanced machine learning algorithms allowed for a nuanced analysis, capturing subtle patterns indicative of early PD stages.

Predictive value of magnetic resonance imaging diffusion parameters using artificial intelligence in low-and intermediate-risk prostate cancer patients treated with stereotactic ablative radiotherapy: A pilot study

IntroductionTo investigate the predictive value of the pre-treatment diffusion parameters of diffusion-weighted magnetic resonance imaging (DW-MRI) using artificial intelligence (AI) for prostate-specific antigen (PSA) response in patients with low- and intermediate-risk prostate cancer (PCa) treated with stereotactic ablative radiotherapy (SABR). MethodsRetrospective evaluation was performed for 30 patients using pre-treatment multi-parametric MR image datasets between 2017 and 2021. MR-based mean- and minimum apparent diffusion coefficients (ADCmean, ADCmin) were calculated for the intraprostatic dominant lesion. Therapeutic response was assessed using PSA levels. Predictive performance was assessed by the receiver operating characteristic (ROC) analysis. Statistics performed with a significance level of p ≤ 0.05. ResultsNo biochemical relapse was detected after a median follow-up of twenty-three months (range: 3–50), with a median PSA of 0.01 ng/ml (range: 0.006–2.8) at the last examination. Significant differences were observed between the pre-treatment ADCmean, ADCmin parameters, and the group averages of patients with low and high 1-year-PSA measurements (p < 0.0001, p < 0.0001). In prediction, the random forest (RF) model outperformed the decision tree (DT) and support vector machine (SVM) models by yielding area under the curves (AUC), with 0.722, 0.685, and 0.5, respectively. ConclusionOur findings suggest that pre-treatment MR diffusion data may predict therapeutic response using the novel approach of machine learning in PCa patients treated with SABR. Implications for practiceClinicians shall measure and implement the evaluation of the suggested parameters (ADCmin, ADCmean) to provide the most accurate therapy for the patient.

An integrated deep learning and supervised learning approach for early detection of brain tumor using magnetic resonance imaging

Diagnosing brain tumors is difficult, especially at an early stage of the disease. Conventional approaches often cause delays in providing required treatment to the patients and shorten their lifespan. This paper presents a novel integrated approach with advanced subsets of artificial intelligence, including deep learning and supervised learning algorithms. These new technologies have demonstrated outstanding potential due to their ability to capture the appropriate features based on the input data. They can assist medical experts in identifying abnormal growth of cells inside the brain. We use publicly available brain magnetic resonance imaging (MRI) datasets to diagnose brain tumors and develop an automated system. The proposed approach uses data augmentation to enhance the image sizes and maintain standardization. We then deploy a visual geometry group with 16 layers following transfer learning to help minimize the medical experts’ workload in making accurate decisions. We extract the most significant features and improve the diagnostic speed and accuracy using a supervised learning algorithm and linear support vector machines (SVM). The proposed model outperforms the existing approaches with an accuracy of 98.87%, precision of 99.09%, recall of 98.73%, specificity of 99.02%, and F1-score of 98.91%.

Imaging segmentation mechanism for rectal tumors using improved U-Net

ObjectiveIn radiation therapy, cancerous region segmentation in magnetic resonance images (MRI) is a critical step. For rectal cancer, the automatic segmentation of rectal tumors from an MRI is a great challenge. There are two main shortcomings in existing deep learning-based methods that lead to incorrect segmentation: 1) there are many organs surrounding the rectum, and the shape of some organs is similar to that of rectal tumors; 2) high-level features extracted by conventional neural networks often do not contain enough high-resolution information. Therefore, an improved U-Net segmentation network based on attention mechanisms is proposed to replace the traditional U-Net network.MethodsThe overall framework of the proposed method is based on traditional U-Net. A ResNeSt module was added to extract the overall features, and a shape module was added after the encoder layer. We then combined the outputs of the shape module and the decoder to obtain the results. Moreover, the model used different types of attention mechanisms, so that the network learned information to improve segmentation accuracy.ResultsWe validated the effectiveness of the proposed method using 3773 2D MRI datasets from 304 patients. The results showed that the proposed method achieved 0.987, 0.946, 0.897, and 0.899 for Dice, MPA, MioU, and FWIoU, respectively; these values are significantly better than those of other existing methods.ConclusionDue to time savings, the proposed method can help radiologists segment rectal tumors effectively and enable them to focus on patients whose cancerous regions are difficult for the network to segment.SignificanceThe proposed method can help doctors segment rectal tumors, thereby ensuring good diagnostic quality and accuracy.

FastMRI Prostate: A public, biparametric MRI dataset to advance machine learning for prostate cancer imaging

Magnetic resonance imaging (MRI) has experienced remarkable advancements in the integration of artificial intelligence (AI) for image acquisition and reconstruction. The availability of raw k-space data is crucial for training AI models in such tasks, but public MRI datasets are mostly restricted to DICOM images only. To address this limitation, the fastMRI initiative released brain and knee k-space datasets, which have since seen vigorous use. In May 2023, fastMRI was expanded to include biparametric (T2- and diffusion-weighted) prostate MRI data from a clinical population. Biparametric MRI plays a vital role in the diagnosis and management of prostate cancer. Advances in imaging methods, such as reconstructing under-sampled data from accelerated acquisitions, can improve cost-effectiveness and accessibility of prostate MRI. Raw k-space data, reconstructed images and slice, volume and exam level annotations for likelihood of prostate cancer are provided in this dataset for 47468 slices corresponding to 1560 volumes from 312 patients. This dataset facilitates AI and algorithm development for prostate image reconstruction, with the ultimate goal of enhancing prostate cancer diagnosis.

Hybrid dual mean-teacher network with double-uncertainty guidance for semi-supervised segmentation of magnetic resonance images

Semi-supervised learning has made significant progress in medical image segmentation. However, existing methods primarily utilize information from a single dimensionality, resulting in sub-optimal performance on challenging magnetic resonance imaging (MRI) data with multiple segmentation objects and anisotropic resolution. To address this issue, we present a Hybrid Dual Mean-Teacher (HD-Teacher) model with hybrid, semi-supervised, and multi-task learning to achieve effective semi-supervised segmentation. HD-Teacher employs a 2D and a 3D mean-teacher network to produce segmentation labels and signed distance fields from the hybrid information captured in both dimensionalities. This hybrid mechanism allows HD-Teacher to utilize features from 2D, 3D, or both dimensions as needed. Outputs from 2D and 3D teacher models are dynamically combined based on confidence scores, forming a single hybrid prediction with estimated uncertainty. We propose a hybrid regularization module to encourage both student models to produce results close to the uncertainty-weighted hybrid prediction to further improve their feature extraction capability. Extensive experiments of binary and multi-class segmentation conducted on three MRI datasets demonstrated that the proposed framework could (1) significantly outperform state-of-the-art semi-supervised methods (2) surpass a fully-supervised VNet trained on substantially more annotated data, and (3) perform on par with human raters on muscle and bone segmentation task. Code will be available at https://github.com/ThisGame42/Hybrid-Teacher.

Simulating rigid head motion artifacts on brain magnitude MRI data-Outcome on image quality and segmentation of the cerebral cortex.

Magnetic Resonance Imaging (MRI) datasets from epidemiological studies often show a lower prevalence of motion artifacts than what is encountered in clinical practice. These artifacts can be unevenly distributed between subject groups and studies which introduces a bias that needs addressing when augmenting data for machine learning purposes. Since unreconstructed multi-channel k-space data is typically not available for population-based MRI datasets, motion simulations must be performed using signal magnitude data. There is thus a need to systematically evaluate how realistic such magnitude-based simulations are. We performed magnitude-based motion simulations on a dataset (MR-ART) from 148 subjects in which real motion-corrupted reference data was also available. The similarity of real and simulated motion was assessed by using image quality metrics (IQMs) including Coefficient of Joint Variation (CJV), Signal-to-Noise-Ratio (SNR), and Contrast-to-Noise-Ratio (CNR). An additional comparison was made by investigating the decrease in the Dice-Sørensen Coefficient (DSC) of automated segmentations with increasing motion severity. Segmentation of the cerebral cortex was performed with 6 freely available tools: FreeSurfer, BrainSuite, ANTs, SAMSEG, FastSurfer, and SynthSeg+. To better mimic the real subject motion, the original motion simulation within an existing data augmentation framework (TorchIO), was modified. This allowed a non-random motion paradigm and phase encoding direction. The mean difference in CJV/SNR/CNR between the real motion-corrupted images and our modified simulations (0.004±0.054/-0.7±1.8/-0.09±0.55) was lower than that of the original simulations (0.015±0.061/0.2±2.0/-0.29±0.62). Further, the mean difference in the DSC between the real motion-corrupted images was lower for our modified simulations (0.03±0.06) compared to the original simulations (-0.15±0.09). SynthSeg+ showed the highest robustness towards all forms of motion, real and simulated. In conclusion, reasonably realistic synthetic motion artifacts can be induced on a large-scale when only magnitude MR images are available to obtain unbiased data sets for the training of machine learning based models.

Sagittal balance parameters measurement on cervical spine MR images based on superpixel segmentation.

Introduction: Magnetic Resonance Imaging (MRI) is essential in diagnosing cervical spondylosis, providing detailed visualization of osseous and soft tissue structures in the cervical spine. However, manual measurements hinder the assessment of cervical spine sagittal balance, leading to time-consuming and error-prone processes. This study presents the Pyramid DBSCAN Simple Linear Iterative Cluster (PDB-SLIC), an automated segmentation algorithm for vertebral bodies in T2-weighted MR images, aiming to streamline sagittal balance assessment for spinal surgeons. Method: PDB-SLIC combines the SLIC superpixel segmentation algorithm with DBSCAN clustering and underwent rigorous testing using an extensive dataset of T2-weighted mid-sagittal MR images from 4,258 patients across ten hospitals in China. The efficacy of PDB-SLIC was compared against other algorithms and networks in terms of superpixel segmentation quality and vertebral body segmentation accuracy. Validation included a comparative analysis of manual and automated measurements of cervical sagittal parameters and scrutiny of PDB-SLIC's measurement stability across diverse hospital settings and MR scanning machines. Result: PDB-SLIC outperforms other algorithms in vertebral body segmentation quality, with high accuracy, recall, and Jaccard index. Minimal error deviation was observed compared to manual measurements, with correlation coefficients exceeding 95%. PDB-SLIC demonstrated commendable performance in processing cervical spine T2-weighted MR images from various hospital settings, MRI machines, and patient demographics. Discussion: The PDB-SLIC algorithm emerges as an accurate, objective, and efficient tool for evaluating cervical spine sagittal balance, providing valuable assistance to spinal surgeons in preoperative assessment, surgical strategy formulation, and prognostic inference. Additionally, it facilitates comprehensive measurement of sagittal balance parameters across diverse patient cohorts, contributing to the establishment of normative standards for cervical spine MR imaging.

Distinctive and Complementary Roles of Default Mode Network Subsystems in Semantic Cognition.

The default mode network (DMN) typically deactivates to external tasks, yet supports semantic cognition. It comprises medial temporal (MT), core, and frontotemporal (FT) subsystems, but its functional organization is unclear: the requirement for perceptual coupling versus decoupling, input modality (visual/verbal), type of information (social/spatial), and control demands all potentially affect its recruitment. We examined the effect of these factors on activation and deactivation of DMN subsystems during semantic cognition, across four task-based human functional magnetic resonance imaging (fMRI) datasets, and localized these responses in whole-brain state space defined by gradients of intrinsic connectivity. FT showed activation consistent with a central role across domains, tasks, and modalities, although it was most responsive to abstract, verbal tasks; this subsystem uniquely showed more "tuned" states characterized by increases in both activation and deactivation when semantic retrieval demands were higher. MT also activated to both perceptually coupled (scenes) and decoupled (autobiographical memory) tasks and showed stronger responses to picture associations, consistent with a role in scene construction. Core DMN consistently showed deactivation, especially to externally oriented tasks. These diverse contributions of DMN subsystems to semantic cognition were related to their location on intrinsic connectivity gradients: activation was closer to the sensory-motor cortex than deactivation, particularly for FT and MT, while activation for core DMN was distant from both visual cortex and cognitive control. These results reveal distinctive yet complementary DMN responses: MT and FT support different memory-based representations that are accessed externally and internally, while deactivation in core DMN is associated with demanding, external semantic tasks.

A Stepwise Multivariate Granger Causality Method for Constructing Hierarchical Directed Brain Functional Network.

The directed brain functional network construction gives us the new insights into the relationships between brain regions from the causality point of view. The Granger causality analysis is one of the powerful methods to model the directed network. The complex brain network is also hierarchically constructed, which is particularly suited to facilitate segregated functions and the global integration of the segregated functions. Therefore, it is of great interest to explore new approach to model the hierarchical architecture of the directed network. In the present study, we proposed a new approach, namely, stepwise multivariate Granger causality (SMGC), considering both the directed and hierarchical features of brain functional network to explore the stepwise causal relationship in the network. The simulation study demonstrated that the diverse and complex hierarchical organization could be embedded in the apparently simple directed network. The proposed SMGC method could capture the multiple hierarchy of the directed network. When applying to the real functional magnetic resonance imaging (fMRI) datasets, the core triple resting-state networks in human brain showed within-network directed connections in the first-level directed network and rich and diverse between-network pathways in the second-level hierarchical network. The default mode network (DMN) had a prominent role in the resting-state acting as both the causal source and the important relay station. Further exploratory research on the adaption of directed hierarchical network in athletes suggested the enhanced bidirectional communication between the DMN and the central executive network (CEN) and the enhanced directed connections from the salience network (SN) to the CEN in the athlete group. The SMGC approach is capable of capturing the hierarchical architecture of the brain directed functional network, which refreshes the new stepwise causal relationship in the directed network. This might shed light on the potential application for exploring the altered hierarchical organization of brain directed network in neuropsychiatric disorders.

A Learnable Counter-Condition Analysis Framework for Functional Connectivity-Based Neurological Disorder Diagnosis.

To understand the biological characteristics of neurological disorders with functional connectivity (FC), recent studies have widely utilized deep learning-based models to identify the disease and conducted post-hoc analyses via explainable models to discover disease-related biomarkers. Most existing frameworks consist of three stages, namely, feature selection, feature extraction for classification, and analysis, where each stage is implemented separately. However, if the results at each stage lack reliability, it can cause misdiagnosis and incorrect analysis in afterward stages. In this study, we propose a novel unified framework that systemically integrates diagnoses (i.e., feature selection and feature extraction) and explanations. Notably, we devised an adaptive attention network as a feature selection approach to identify individual-specific disease-related connections. We also propose a functional network relational encoder that summarizes the global topological properties of FC by learning the inter-network relations without pre-defined edges between functional networks. Last but not least, our framework provides a novel explanatory power for neuroscientific interpretation, also termed counter-condition analysis. We simulated the FC that reverses the diagnostic information (i.e., counter-condition FC): converting a normal brain to be abnormal and vice versa. We validated the effectiveness of our framework by using two large resting-state functional magnetic resonance imaging (fMRI) datasets, Autism Brain Imaging Data Exchange (ABIDE) and REST-meta-MDD, and demonstrated that our framework outperforms other competing methods for disease identification. Furthermore, we analyzed the disease-related neurological patterns based on counter-condition analysis.

Integration of graph network with kernel SVM and logistic regression for identification of biomarkers in SCA12 and its diagnosis.

Spinocerebellar ataxia type 12 is a hereditary and neurodegenerative illness commonly found in India. However, there is no established noninvasive automatic diagnostic system for its diagnosis and identification of imaging biomarkers. This work proposes a novel four-phase machine learning-based diagnostic framework to find spinocerebellar ataxia type 12 disease-specific atrophic-brain regions and distinguish spinocerebellar ataxia type 12 from healthy using a real structural magnetic resonance imaging dataset. Firstly, each brain region is represented in terms of statistics of coefficients obtained using 3D-discrete wavelet transform. Secondly, a set of relevant regions are selected using a graph network-based method. Thirdly, a kernel support vector machine is used to capture nonlinear relationships among the voxels of a brain region. Finally, the linear relationship among the brain regions is captured to build a decision model to distinguish spinocerebellar ataxia type 12 from healthy by using the regularized logistic regression method. A classification accuracy of 95% and a harmonic mean of precision and recall, i.e. F1-score of 94.92%, is achieved. The proposed framework provides relevant regions responsible for the atrophy. The importance of each region is captured using Shapley Additive exPlanations values. We also performed a statistical analysis to find volumetric changes in spinocerebellar ataxia type 12 group compared to healthy. The promising result of the proposed framework shows that clinicians can use it for early and timely diagnosis of spinocerebellar ataxia type 12.