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Manual segmentation of brain tumors using structural magnetic resonance imaging (MRI) is an arduous and time-consuming task. Therefore, automatic and robust segmentation will considerably influence neuro-oncological clinical trials by reducing excessive manual annotation time. Herein, we propose a deep learning model that automatically segments brain tumors even in cases of missing MRI sequences, which are common in practical clinical settings. To address this issue, we enhance a generative adversarial network (GAN) by incorporating a squeeze-and-excitation (SE) attention module into its generator and a PatchGAN into its discriminator. The SE module recalibrates channel responses by explicitly modeling interdependencies, enabling the network to focus on critical regions such as tumor areas. Our proposed generative model is optimized using a combination of adversarial, structural similarity, and mean absolute error losses to synthesize missing MRI sequences more effectively. This enhancement allows our model to synthesize the missing MRI sequence (fluid attenuated inversion recovery [FLAIR]) by leveraging information from other available sequences (T1-weighted, T2-weighted, or contrast-enhanced T1-weighted [T1ce]). For the segmentation task, we employ an optimized nnU-Net model, which is trained using existing sequences and evaluated using both available and synthesized sequences (including missing ones), mimicking real-world scenarios where often only limited MRI sequences are available or usable. Our findings reveal a notable enhancement in brain tumor segmentation, as indicated by a significant increase in overall the Dice similarity coefficient (DSC) from 0.688% (when FLAIR is missing) to 0.873% (when using synthesized FLAIR derived from T2). This improvement brings the segmentation performance closer to what was achieved when real FLAIR was available, where the DSC reaches 0.901%. Moreover, our synthesizing model was also tested on two additional datasets: the BraTS 2020 validation set and BraTS Africa 2023 training set, which produces results comparable to those of BraTS 2021, thereby proving its robustness and generalizability. In addition, the resulting tumor segmentations are subsequently employed to assess the response to treatment in cases where all sequences were available and when synthesis was employed, according to response assessment in neuro-oncology criteria. [Display omitted] [ABSTRACT FROM AUTHOR]

Magnetic resonance electrical properties tomography (MR‐EPT) is a non‐invasive measurement technique that derives the electrical properties (EPs, e.g., conductivity or permittivity) of tissues in the radiofrequency range (64 MHz for 1.5 T and 128 MHz for 3 T MR systems). Clinical studies have shown the potential of tissue conductivity as a biomarker. To date, model‐based conductivity reconstructions rely on numerical assumptions and approximations, leading to inaccuracies in the reconstructed maps. To address such limitations, we propose an artificial neural network (ANN)‐based non‐linear conductivity estimator trained on simulated data for conductivity brain imaging. Network training was performed on 201 synthesized T2‐weighted spin‐echo (SE) data obtained from the finite‐difference time‐domain (FDTD) electromagnetic (EM) simulation. The dataset was composed of an approximated T2‐w SE magnitude and transceive phase information. The proposed method was tested three in‐silico and in‐vivo on two volunteers and three patients' data. For comparison purposes, various conventional phase‐based EPT reconstruction methods were used that ignore B1+ magnitude information, such as Savitzky–Golay kernel combined with Gaussian filter (S‐G Kernel), phase‐based convection‐reaction EPT (cr‐EPT), magnitude‐weighted polynomial‐fitting phase‐based EPT (Poly‐Fit), and integral‐based phase‐based EPT (Integral‐based). From the in‐silico experiments, quantitative analysis showed that the proposed method provides more accurate and improved quality (e.g., high structural preservation) conductivity maps compared to conventional reconstruction methods. Representatively, in the healthy brain in‐silico phantom experiment, the proposed method yielded mean conductivity values of 1.97 ± 0.20 S/m for CSF, 0.33 ± 0.04 S/m for WM, and 0.52 ± 0.08 S/m for GM, which were closer to the ground‐truth conductivity (2.00, 0.30, 0.50 S/m) than the integral‐based method (2.56 ± 2.31, 0.39 ± 0.12, 0.68 ± 0.33 S/m). In‐vivo ANN‐based conductivity reconstructions were also of improved quality compared to conventional reconstructions and demonstrated network generalizability and robustness to in‐vivo data and pathologies. The reported in‐vivo brain conductivity values were in agreement with literatures. In addition, the proposed method was observed for various SNR levels (SNR levels = 10, 20, 40, and 58) and repeatability conditions (the eight acquisitions with the number of signal averages = 1). The preliminary investigations on brain tumor patient datasets suggest that the network trained on simulated dataset can generalize to unforeseen in‐vivo pathologies, thus demonstrating its potential for clinical applications. [ABSTRACT FROM AUTHOR]

Medical image segmentation of tissue abnormalities, key organs, or blood vascular system is of great significance for any computerized diagnostic system. However, automatic segmentation in medical image analysis is a challenging task since it requires sophisticated knowledge of the target organ anatomy. This paper develops an end-to-end deep learning segmentation method called Contextual Multi-Scale Multi-Level Network (CMM-Net). The main idea is to fuse the global contextual features of multiple spatial scales at every contracting convolutional network level in the U-Net. Also, we re-exploit the dilated convolution module that enables an expansion of the receptive field with different rates depending on the size of feature maps throughout the networks. In addition, an augmented testing scheme referred to as Inversion Recovery (IR) which uses logical "OR" and "AND" operators is developed. The proposed segmentation network is evaluated on three medical imaging datasets, namely ISIC 2017 for skin lesions segmentation from dermoscopy images, DRIVE for retinal blood vessels segmentation from fundus images, and BraTS 2018 for brain gliomas segmentation from MR scans. The experimental results showed superior state-of-the-art performance with overall dice similarity coefficients of 85.78%, 80.27%, and 88.96% on the segmentation of skin lesions, retinal blood vessels, and brain tumors, respectively. The proposed CMM-Net is inherently general and could be efficiently applied as a robust tool for various medical image segmentations. [ABSTRACT FROM AUTHOR]

• We develop a single-stage knowledge distillation framework that successively trains the teacher and student networks in the same training iteration, which can be used for brain tumor segmentation on limited MR modality. • As a practical verification of the feasibility of the proposed segmentation approach to be generalized to clinical usage, we further test our model using brain dataset collected from the local hospital. • Experimental results of proposed model are better than other benchmark methods on both the BraTS dataset and our local dataset. Precisely segmenting brain tumors using multimodal Magnetic Resonance Imaging (MRI) is an essential task for early diagnosis, disease monitoring, and surgical planning. Unfortunately, the complete four image modalities utilized in the well-known BraTS benchmark dataset: T1, T2, Fluid-Attenuated Inversion Recovery (FLAIR), and T1 Contrast-Enhanced (T1CE) are not regularly acquired in clinical practice due to the high cost and long acquisition time. Rather, it is common to utilize limited image modalities for brain tumor segmentation. In this paper, we propose a single stage learning of knowledge distillation algorithm that derives information from the missing modalities for better segmentation of brain tumors. Unlike the previous works that adopted a two-stage framework to distill the knowledge from a pre-trained network into a student network, where the latter network is trained on limited image modality, we train both models simultaneously using a single-stage knowledge distillation algorithm. We transfer the information by reducing the redundancy from a teacher network trained on full image modalities to the student network using Barlow Twins loss on a latent-space level. To distill the knowledge on the pixel level, we further employ a deep supervision idea that trains the backbone networks of both teacher and student paths using Cross-Entropy loss. We demonstrate that the proposed single-stage knowledge distillation approach enables improving the performance of the student network in each tumor category with overall dice scores of 91.11% for Tumor Core, 89.70% for Enhancing Tumor, and 92.20% for Whole Tumor in the case of only using the FLAIR and T1CE images, outperforming the state-of-the-art segmentation methods. The outcomes of this work prove the feasibility of exploiting the knowledge distillation in segmenting brain tumors using limited image modalities and hence make it closer to clinical practices. [Display omitted] [ABSTRACT FROM AUTHOR]