In recent years, several deep learning models have been proposed to accurately quantify and diagnose cardiac pathologies. These automated tools heavily rely on the accurate segmentation of cardiac structures in MRI images. However, segmentation of the right ventricle is challenging due to its highly complex shape and ill-defined borders. Hence, there is a need for new methods to handle such structure's geometrical and textural complexities, notably in the presence of pathologies such as Dilated Right Ventricle, Tricuspid Regurgitation, Arrhythmogenesis, Tetralogy of Fallot, and Inter-atrial Communication. The last MICCAI challenge on right ventricle segmentation was held in 2012 and included only 48 cases from a single clinical center. As part of the 12 th Workshop on Statistical Atlases and Computational Models of the Heart (STACOM 2021), the M&Ms-2 challenge was organized to promote the interest of the research community around right ventricle segmentation in multi-disease, multi-view, and multi-center cardiac MRI. Three hundred sixty CMR cases, including short-axis and long-axis 4-chamber views, were collected from three Spanish hospitals using nine different scanners from three different vendors, and included a diverse set of right and left ventricle pathologies. The solutions provided by the participants show that nnU-Net achieved the best results overall. However, multi-view approaches were able to capture additional information, highlighting the need to integrate multiple cardiac diseases, views, scanners, and acquisition protocols to produce reliable automatic cardiac segmentation algorithms.
Assessing cognitive load during a learning phase is important, as it assists to understand the complexity of the learning task. It can help in balancing the cognitive load of postlearning and during the actual task. Here, we used electroencephalography (EEG) to assess cognitive load in multimedia learning task. EEG data were collected from 34 human participants at baseline and a multimedia learning state. The analysis was based on feature extraction and partial directed coherence (PDC). Results revealed that the EEG frequency bands and activated brain regions that contribute to cognitive load differed depending on the learning state. We concluded that cognitive load during multimedia learning can be assessed using feature extraction and measures of effective connectivity (PDC).
14 March 2023 in IEEE/ACM Transactions on Computational Biology and Bioinformatics
Depression is a mental disorder characterized by persistent depressed mood or loss of interest in performing activities, causing significant impairment in daily routine. Possible causes include psychological, biological, and social sources of distress. Clinical depression is the more-severe form of depression, also known as major depression or major depressive disorder. Recently, electroencephalography and speech signals have been used for early diagnosis of depression; however, they focus on moderate or severe depression. We have combined audio spectrogram and multiple frequencies of EEG signals to improve diagnostic performance. To do so, we have fused different levels of speech and EEG features to generate descriptive features and applied vision transformers and various pre-trained networks on the speech and EEG spectrum. We have conducted extensive experiments on Multimodal Open Dataset for Mental-disorder Analysis (MODMA) dataset, which showed significant improvement in performance in depression diagnosis ( 0.972 , 0.973 and 0.973 precision, recall and F1 score respectively ) for patients at the mild stage. Besides, we provided a web-based framework using Flask and provided the source code publicly https://github.com/RespectKnowledge/EEG_Speech_Depression_MultiDL .
30 October 2024 in IEEE Transactions on Medical Imaging
Segmentation is a critical step in analyzing the developing human fetal brain. There have been vast improvements in automatic segmentation methods in the past several years, and the Fetal Brain Tissue Annotation (FeTA) Challenge 2021 helped to establish an excellent standard of fetal brain segmentation. However, FeTA 2021 was a single center study, limiting real-world clinical applicability and acceptance. The multi-center FeTA Challenge 2022 focused on advancing the generalizability of fetal brain segmentation algorithms for magnetic resonance imaging (MRI). In FeTA 2022, the training dataset contained images and corresponding manually annotated multi-class labels from two imaging centers, and the testing data contained images from these two centers as well as two additional unseen centers. The multi-center data included different MR scanners, imaging parameters, and fetal brain super-resolution algorithms applied. 16 teams participated and 17 algorithms were evaluated. Here, the challenge results are presented, focusing on the generalizability of the submissions. Both in- and out-of-domain, the white matter and ventricles were segmented with the highest accuracy (Top Dice scores: 0.89, 0.87 respectively), while the most challenging structure remains the grey matter (Top Dice score: 0.75) due to anatomical complexity. The top 5 average Dices scores ranged from 0.81-0.82, the top 5 average 95 th percentile Hausdorff distance values ranged from 2.3-2.5mm, and the top 5 volumetric similarity scores ranged from 0.90-0.92. The FeTA Challenge 2022 was able to successfully evaluate and advance generalizability of multi-class fetal brain tissue segmentation algorithms for MRI and it continues to benchmark new algorithms.
Computed tomography (CT) with a contrast-enhanced imaging technique is extensively proposed for the assessment and segmentation of multiple organs, especially organs at risk. It is an important factor involved in the decision making in clinical applications. Automatic segmentation and extraction of abdominal organs, such as thoracic organs at risk, from CT images are challenging tasks due to the low contrast of pixel values surrounding other organs. Various deep learning models based on 2D and 3D convolutional neural networks have been proposed for the segmentation of medical images because of their automatic feature extraction capability based on large labeled datasets. In this paper, we proposed a 3D-atrous spatial pyramid pooling (ASPP) module integrated with a proposed 3D DensNet encoder–decoder network for volumetric segmentation to segment abdominal organs from CT. The proposed network used a 3D-ASPP block to capture spatial information in multiscale input feature maps from the decoder side. We also proposed a 3D-ASPP block with a 3D DensNet network for automatically processing 3D medical volumetric images. The proposed hybrid network was named 3D-ASPPDN for volumetric segmentation via CT medical imaging. We tested our proposed approach on a public dataset, Thoracic Organs at Risk (SegTHOR) 2019. The proposed solution showed excellent performance in comparison with other existing state-of-the-art DL methods. The proposed method achieved Dice scores 97.89% on the SegTHOR dataset. Results presented that 3D-ASPPDN exhibited enhanced performance in volumetric biomedical segmentation. The proposed model could be used for volumetric segmentation in clinical applications to diagnose problems in multi class organs.
12 December 2023 in IEEE Journal of Biomedical and Health Informatics
The availability of large, high-quality annotated datasets in the medical domain poses a substantial challenge in segmentation tasks. To mitigate the reliance on annotated training data, self-supervised pre-training strategies have emerged, particularly employing contrastive learning methods on dense pixel-level representations. In this work, we proposed to capitalize on intrinsic anatomical similarities within medical image data and develop a semantic segmentation framework through a self-supervised fusion network, where the availability of annotated volumes is limited. In a unified training phase, we combine segmentation loss with contrastive loss, enhancing the distinction between significant anatomical regions that adhere to the available annotations. To further improve the segmentation performance, we introduce an efficient parallel transformer module that leverages Multiview multiscale feature fusion and depth-wise features. The proposed transformer architecture, based on multiple encoders, is trained in a self-supervised manner using contrastive loss. Initially, the transformer is trained using an unlabeled dataset. We then fine-tune one encoder using data from the first stage and another encoder using a small set of annotated segmentation masks. These encoder features are subsequently concatenated for the purpose of brain tumor segmentation. The multiencoder-based transformer model yields significantly better outcomes across three medical image segmentation tasks. We validated our proposed solution by fusing images across diverse medical image segmentation challenge datasets, demonstrating its efficacy by outperforming state-of-the-art methodologies.