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PCcS-RAU-Net: Automated parcellated Corpus callosum segmentation from brain MRI images using modified residual attention U-Net

Chandra Anjali, Verma Shrish, Raghuvanshi A.S., Kuber Bodhey Narendra

Biocybernetics and Biomedical Engineering

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2023

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Vol. 43, no. 2

403--427

EN

Background: The Corpus callosum (Cc) in the cerebral cortex is a bundle of neural fibers that facilitates inter-hemispheric communication. The Cc area and area of its sub-regions (also known as parcels) have been examined as a biomarker for cortical pathology and differential diagnosis in neurodegenerative diseases such as Autism, Alzheimer’s disease (AD), and more. Manual segmentation and parcellation of Cc are laborious and time-consuming. The present work proposes a novel work of automated parcellated Cc (PCc) segmentation that will serve as a potential biomarker to study and diagnose neurological disorders in brain MRI images. Method: In this perspective, the present work aims to develop an automated PCc segmentation from mid-sagittal T1- weighted (w) 2D brain MRI images using a deep learning-based fully convolutional network, a modified residual attention U-Net, referred to as PCcS-RAU-Net. The model has been modified to use a multi-class segmentation configuration with five target classes (parcels): rostrum, genu, mid-body, isthmus and splenium. Results: The experimental research uses two benchmark MRI datasets, ABIDE and OASIS. The proposed PCcS-RAU-Net outperformed existing methods on the ABIDE dataset with a DSC of 97.10% and MIoU of 94.43%. Furthermore, the model’s performance is validated on the OASIS and Real clinical image (RCI) data and hence verifies the model’s generalization capability. Conclusion: The proposed PCcS-RAU-Net model extracts essential characteristics such as the total area of the Cc (TCcA) to categorize MRI slices into healthy controls (HC) and disease groups. Also, sub-regional areas, Cc1A to Cc5A, help study atrophy progression for early diagnosis.

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CCsNeT: Automated Corpus Callosum segmentation using fully convolutional network based on U-Net

Chandra Anjali, Verma Shrish, Raghuvanshi A.S., Bodhey Narendra Kuber

Biocybernetics and Biomedical Engineering

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2022

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Vol. 42, no. 1

187--203

EN

Background: Corpus Callosum (CC) is the most prominent white matter bundle in the human brain that connects the left and right cerebral hemispheres. The present paper proposes a novel method for CC segmentation from 2D T1- weighted mid-sagittal brain MRI. The robust segmentation of CC in the mid-sagittal plane plays a vital role in the quantitative study of CC structural features related to various neurological disorders such as Autism, epilepsy, Alzheimer’s disease, and more. Methodology: In this perspective, the current work proposes a Fully Convolutional Network (FCN), a deep learning architecture-based U-Net model for automated CC segmentation from 2D brain MRI images referred to as CCsNeT. The architecture consists of a 35-layers deep, fully convolutional network with two paths, namely contracting and extracting, connected in a U-shape that automatically extracts spatial information. Results: This attempt uses the benchmark brain MRI database comprising ABIDE and OASIS for the experimental investigation. Compared to existing CC segmentation methodologies, the proposed CCsNeT presented improved results achieving Dice Coefficient = 96.74%, and Sensitivity = 97.01% with ABIDE dataset and were further validated against the variants of U-Net model U-Net++, MultiResU-Net, and CE-Net. Further, the performance of CCsNeT has been validated on OASIS and Real-Time Images dataset. Conclusion: Finally, the proposed CCsNeT extracts important CC characteristics such as CC area (CCA) and total brain area (TBA) to categorize the considered 2D MRI slices into control and autism spectrum disorder (ASD) groups, thereby minimizing the inter-observer and intra-observer variability.

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Mediastinal lymph node malignancy detection in computed tomography images using fully convolutional network

Tekchandani Hitesh, Verma Shrish, Londhe Narendra D.

Biocybernetics and Biomedical Engineering

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2020

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Vol. 40, no. 1

187--199

EN

Differential diagnosis of malignant and benign mediastinal lymph nodes (LNs) through invasive pathological tests is a complex and painful procedure because of sophisticated anatomical locations of LNs in the chest. The image based automatic machine learning techniques have been attempted in the past for malignancy detection. But these conventional methods suffer from complex selection of hand-crafted features and trade-off between performance parameters due to them. Today deep learning approaches are out-performing conventional machine learning techniques and able to overcome these issues. However, the existing convolutional neural network (CNN) based models also are prone to overfitting because of fully connected (FC) layers. Therefore, in this paper authors have proposed a fully convolutional network (FCN) based deep learning model for lymph nodes malignancy detection in computed tomography (CT) images. Moreover, the proposed FCN has been customized with batch normalization and advanced activation function Leaky ReLU to accelerate the training and to overcome the problem of dying ReLU, respectively. The performance of the proposed FCN has been also tuned to its best for smaller data size using data augmentation methods. The generalization of the proposed model is tested using the network parameter variation. To understand the reliability of the proposed model, it has also been compared with state-of-art related deep learning networks. The proposed FCN model has achieved an average accuracy, sensitivity, specificity, and area under curve as 90.28%, 90.63%, 89.95%, and 0.90, respectively. Our results also confirms the successful usabilility of augmentation methods for working on smaller datasets and deep learning approaches.