BAI-Net: Individualized Anatomical Cerebral Cartography Using Graph Neural Network

A systematic review of resting-state functional-MRI studies in the diagnosis, comorbidity and treatment of postpartum depression

BACKGROUND

Postpartum depression (PPD) is a common and serious mental health problem that affects many new mothers and their families worldwide. In recent years, there has been an increasing number of studies using magnetic resonance techniques (MRI), particularly functional MRI (fMRI), to explore the neuroimaging biomarker of this disease.

METHODS

PubMed database was used to search for English literature focusing on resting-state fMRI and PPD published up to June 2024.

RESULTS

After screening, 17 studies were finally identified, among which all 17 studies reported abnormal regions or connectivity compared to health controls (HC), 4 studies reported results considering the differences between PPD and PPD with anxiety (PPD-A), and 2 studies reported biomarkers for the treatment of PPD. The existing studies indicate that PPD is characterized by functional impairments in multiple brain regions, especially the medial prefrontal cortex (MPFC), precentral gyrus and cerebellum. Abnormal functional connectivity has been widely reported in the dorsomedial prefrontal cortex (dmPFC), anterior cingulate cortex (ACC) and the orbitofrontal cortex (OFC). However, none of the four comorbidity studies identified overlapping discriminative biomarkers between PPD and PPD-A. Additionally, the two treatment-related studies consistently reported functional improvements in the amygdala after effective treatment.

CONCLUSION

The affected brain regions were highly overlapped with major depressive disorder (MDD), suggesting that PPD may be categorized as a potential subtype of MDD. Considering the negative effects of medication on PPD, future efforts should focus on developing non-pharmacological therapies, such as transcranial magnetic stimulation (TMS) and acupuncture, to support women with PPD in overcoming this unique and important phase.

Parcellation of individual brains: From group level atlas to precise mapping

Individual brains vary greatly in morphology, connectivity, and organization. Group-level brain parcellations, which do not account for individual variations in brain parcels, are increasingly limited in their applicability, especially given the rapid development of precision medicine. Accurate individual-level brain functional mapping is pivotal for comprehending variations in brain functions and behaviors, the early and precise identification of brain abnormalities, and personalized treatments for neuropsychiatric disorders. Recent advances in neuroimaging and machine learning techniques have led to a surge in studies on the parcellation of individual brains. In this paper, we present an overview of recent advances in the methodologies of individual brain parcellation, including optimization- and learning-based methods. We then introduce comprehensive evaluation metrics to validate individual functional regions, and discuss how individual brain mapping advances neuroscience research and clinical medicine. Finally, major challenges and future directions of individual brain parcellation are summarized. In conclusion, we provide a comprehensive overview of individual brain parcellation methods, validations, and applications, highlighting current challenges and the urgent need for integrated platforms that encompass datasets, methods, and validations.

BIGFormer: A Graph Transformer With Local Structure Awareness for Diagnosis and Pathogenesis Identification of Alzheimer's Disease Using Imaging Genetic Data

Alzheimer's disease (AD) is a highly inheritable neurological disorder, and brain imaging genetics (BIG) has become a rapidly advancing field for comprehensive understanding its pathogenesis. However, most of the existing approaches underestimate the complexity of the interactions among factors that cause AD. To take full appreciate of these complexity interactions, we propose BIGFormer, a graph Transformer with local structural awareness, for AD diagnosis and identification of pathogenic mechanisms. Specifically, the factors interaction graph is constructed with lesion brain regions and risk genes as nodes, where the connection between nodes intuitively represents the interaction between nodes. After that, a perception with local structure awareness is built to extract local structure around nodes, which is then injected into node representation. Then, the global reliance inference component assembles the local structure into higher-order structure, and multi-level interaction structures are jointly aggregated into a classification projection head for disease state prediction. Experimental results show that BIGFormer demonstrated superiority in four classification tasks on the AD neuroimaging initiative dataset and proved to identify biomarkers closely intimately related to AD.

TS-AI: A deep learning pipeline for multimodal subject-specific parcellation with task contrasts synthesis

Accurate mapping of brain functional subregions at an individual level is crucial. Task-based functional MRI (tfMRI) captures subject-specific activation patterns during various functions and behaviors, facilitating the individual localization of functionally distinct subregions. However, acquiring high-quality tfMRI is time-consuming and resource-intensive in both scientific and clinical settings. The present study proposes a two-stage network model, TS-AI, to individualize an atlas on cortical surfaces through the prediction of tfMRI data. TS-AI first synthesizes a battery of task contrast maps for each individual by leveraging tract-wise anatomical connectivity and resting-state networks. These synthesized maps, along with feature maps of tract-wise anatomical connectivity and resting-state networks, are then fed into an end-to-end deep neural network to individualize an atlas. TS-AI enables the synthesized task contrast maps to be used in individual parcellation without the acquisition of actual task fMRI scans. In addition, a novel feature consistency loss is designed to assign vertices with similar features to the same parcel, which increases individual specificity and mitigates overfitting risks caused by the absence of individual parcellation ground truth. The individualized parcellations were validated by assessing test-retest reliability, homogeneity, and cognitive behavior prediction using diverse reference atlases and datasets, demonstrating the superior performance and generalizability of TS-AI. Sensitivity analysis yielded insights into region-specific features influencing individual variation in functional regionalization. Additionally, TS-AI identified accelerated shrinkage in the medial temporal and cingulate parcels during the progression of Alzheimer's disease, suggesting its potential in clinical research and applications.

D-MHGCN: An End-to-End Individual Behavioral Prediction Model Using Dual Multi-Hop Graph Convolutional Network

Predicting individual behavior is a crucial area of research in neuroscience. Graph Neural Networks (GNNs), as powerful tools for extracting graph-structured features, are increasingly being utilized in various functional connectivity (FC) based behavioral prediction tasks. However, current predictive models primarily focus on enhancing GNNs' ability to extract features from FC networks while neglecting the importance of upstream individual network construction quality. This oversight results in constructed functional networks that fail to adequately represent individual behavioral capacity, thereby affecting the subsequent prediction accuracy. To address this issue, we proposed a new GNN-based behavioral prediction framework, named Dual Multi-Hop Graph Convolutional Network (D-MHGCN). Through the joint training of two GCNs, this framework integrates individual functional network construction and behavioral prediction into a unified optimization model. It allows the model to dynamically adjust the individual functional cortical parcellation according to the downstream tasks, thus creating task-aware, individual-specific FCNs that largely enhance its ability to predict behavior scores. Additionally, we employed multi-hop graph convolution layers instead of traditional single-hop methods in GCN to capture complex hierarchical connectivity patterns in brain networks. Our experimental evaluations, conducted on the large, public Human Connectome Project dataset, demonstrate that our proposed method outperforms existing methods in various behavioral prediction tasks. Moreover, it produces more functionally homogeneous cortical parcellation, showcasing its practical utility and effectiveness. Our work not only enhances the accuracy of individual behavioral prediction but also provides deeper insights into the neural mechanisms underlying individual differences in behavior.

Multimodal Connectivity-Based Individual Parcellation and Analysis for Humans and Rhesus Monkeys

Individual brains vary greatly in morphology, connectivity and organization. Individualized brain parcellation is capable of precisely localizing subject-specific functional regions. However, most individualization approaches have examined single modalities of data and have not generalized to nonhuman primates. The present study proposed a novel multimodal connectivity-based individual parcellation (MCIP) method, which optimizes within-region homogeneity, spatial continuity and similarity to a reference atlas with the fusion of personal functional and anatomical connectivity. Comprehensive evaluation demonstrated that MCIP outperformed state-of-the-art multimodal individualization methods in terms of functional and anatomical homogeneity, predictability of cognitive measures, heritability, reproducibility and generalizability across species. Comparative investigation showed a higher topographic variability in humans than that in macaques. Therefore, MCIP provides improved accurate and reliable mapping of brain functional regions over existing methods at an individual level across species, and could facilitate comparative and translational neuroscience research.

Individualized brain mapping for navigated neuromodulation

ABSTRACT

The brain is a complex organ that requires precise mapping to understand its structure and function. Brain atlases provide a powerful tool for studying brain circuits, discovering biological markers for early diagnosis, and developing personalized treatments for neuropsychiatric disorders. Neuromodulation techniques, such as transcranial magnetic stimulation and deep brain stimulation, have revolutionized clinical therapies for neuropsychiatric disorders. However, the lack of fine-scale brain atlases limits the precision and effectiveness of these techniques. Advances in neuroimaging and machine learning techniques have led to the emergence of stereotactic-assisted neurosurgery and navigation systems. Still, the individual variability among patients and the diversity of brain diseases make it necessary to develop personalized solutions. The article provides an overview of recent advances in individualized brain mapping and navigated neuromodulation and discusses the methodological profiles, advantages, disadvantages, and future trends of these techniques. The article concludes by posing open questions about the future development of individualized brain mapping and navigated neuromodulation.

Prior-guided individualized thalamic parcellation based on local diffusion characteristics

Comprising numerous subnuclei, the thalamus intricately interconnects the cortex and subcortex, orchestrating various facets of brain functions. Extracting personalized parcellation patterns for these subnuclei is crucial, as different thalamic nuclei play varying roles in cognition and serve as therapeutic targets for neuromodulation. However, accurately delineating the thalamic nuclei boundary at the individual level is challenging due to intersubject variability. In this study, we proposed a prior-guided parcellation (PG-par) method to achieve robust individualized thalamic parcellation based on a central-boundary prior. We first constructed probabilistic atlas of thalamic nuclei using high-quality diffusion MRI datasets based on the local diffusion characteristics. Subsequently, high-probability voxels in the probabilistic atlas were utilized as prior guidance to train unique multiple classification models for each subject based on a multilayer perceptron. Finally, we employed the trained model to predict the parcellation labels for thalamic voxels and construct individualized thalamic parcellation. Through a test-retest assessment, the proposed prior-guided individualized thalamic parcellation exhibited excellent reproducibility and the capacity to detect individual variability. Compared with group atlas registration and individual clustering parcellation, the proposed PG-par demonstrated superior parcellation performance under different scanning protocols and clinic settings. Furthermore, the prior-guided individualized parcellation exhibited better correspondence with the histological staining atlas. The proposed prior-guided individualized thalamic parcellation method contributes to the personalized modeling of brain parcellation.