scholarly journals Deep Learning with Limited Data: Organ Segmentation Performance by U-Net

Electronics ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1199
Author(s):  
Michelle Bardis ◽  
Roozbeh Houshyar ◽  
Chanon Chantaduly ◽  
Alexander Ushinsky ◽  
Justin Glavis-Bloom ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Deep Learning ◽  
Magnetic Resonance ◽  
Data Availability ◽  
Resonance Imaging ◽  
Learning Network ◽  
Transrectal Biopsy ◽  
Minimum Number ◽  
Magnetic Resonance Imaging Mri ◽  
Deep Learning Network

(1) Background: The effectiveness of deep learning artificial intelligence depends on data availability, often requiring large volumes of data to effectively train an algorithm. However, few studies have explored the minimum number of images needed for optimal algorithmic performance. (2) Methods: This institutional review board (IRB)-approved retrospective review included patients who received prostate magnetic resonance imaging (MRI) between September 2014 and August 2018 and a magnetic resonance imaging (MRI) fusion transrectal biopsy. T2-weighted images were manually segmented by a board-certified abdominal radiologist. Segmented images were trained on a deep learning network with the following case numbers: 8, 16, 24, 32, 40, 80, 120, 160, 200, 240, 280, and 320. (3) Results: Our deep learning network’s performance was assessed with a Dice score, which measures overlap between the radiologist’s segmentations and deep learning-generated segmentations and ranges from 0 (no overlap) to 1 (perfect overlap). Our algorithm’s Dice score started at 0.424 with 8 cases and improved to 0.858 with 160 cases. After 160 cases, the Dice increased to 0.867 with 320 cases. (4) Conclusions: Our deep learning network for prostate segmentation produced the highest overall Dice score with 320 training cases. Performance improved notably from training sizes of 8 to 120, then plateaued with minimal improvement at training case size above 160. Other studies utilizing comparable network architectures may have similar plateaus, suggesting suitable results may be obtainable with small datasets.

scholarly journals Diagnosa Tumor Otak Berdasarkan Citra MRI (Magnetic Resonance Imaging)

2019 ◽  
Vol 18 (2) ◽  
Author(s):  
Ida Bagus Leo Mahadya Suta ◽  
Rukmi Sari Hartati ◽  
Yoga Divayana
Keyword(s):  
Neural Network ◽  
Magnetic Resonance Imaging ◽  
Deep Learning ◽  
Magnetic Resonance ◽  
Convolutional Neural Network ◽  
Resonance Imaging ◽  
Magnetic Resonance Imaging Mri

Tumor otak menjadi salah satu penyakit yang paling mematikan, salah satu jenis yang paling banyak ditemukan adalah glioma sekitar 6 dari 100.000 pasien adalah penderita glioma. Citra digital melalui Magnetic Resonance Imaging (MRI) merupakan salah satu metode untuk membantu dokter dalam menganalisa dan mengklasifikasikan jenis tumor otak. Namun, klasifikasi secara manual membutuhkan waktu yang lama dan memiliki resiko kesalahan yang tinggi, untuk itu dibutuhkan suatu cara otomatis dan akurat dalam melakukan klasifikasi citra MRI. Convolutional Neural Network (CNN) menjadi salah satu solusi dalam melakukan klasifikasi otomatis dalam citra MRI. CNN merupakan algoritma deep learning yang memiliki kemampuan untuk belajar sendiri dari kasus kasus sebelumnya. Dan dari penelitian yang telah dilakukan, diperoleh hasil bahwa CNN mampu dalam menyelesaikan klasifikasi tumor otak dengan akurasi yang tinggi. Peningkatan akurasi diperoleh dengan mengembangkan algoritma CNN baik melalui menentukan nilai kernel dan/atau fungsi aktivasi.

scholarly journals Brain Tumor Classification using Deep Learning Algorithms

2021 ◽  
Vol 9 (12) ◽  
pp. 417-426
Author(s):  
Ankita Kadam
Keyword(s):  
Neural Network ◽  
Magnetic Resonance Imaging ◽  
Neural Networks ◽  
Deep Learning ◽  
Brain Tumor ◽  
Magnetic Resonance ◽  
Brain Tumors ◽  
Tumor Classification ◽  
Resonance Imaging ◽  
Magnetic Resonance Imaging Mri

Abstract: A Brain tumor is one aggressive disease. An estimated more than 84,000 people will receive a primary brain tumor diagnosis in 2021 and an estimated 18,600 people will die from a malignant brain tumor (brain cancer) in 2021.[8] The best technique to detect brain tumors is by using Magnetic Resonance Imaging (MRI). More than any other cancer, brain tumors can have lasting and life-altering physical, cognitive, and psychological impacts on a patient’s life and hence faster diagnosis and best treatment plan should be devised to improve the life expectancy and well-being of these patients. Neural networks have shown colossal accuracy in image classification and segmentation problems. In this paper, we propose comparative studies of various deep learning models based on different types of Neural Networks(ANN, CNN, TL) to firstly identify brain tumors and then classify them into Benign Tumor, Malignant Tumor or Pituitary Tumor. The data set used holds 3190 images on T1-weighted contrast-enhanced images which were cleaned and augmented. The best ANN model concluded with an accuracy of 78% and the best CNN model consisting of 3 convolution layers had an accuracy of 90%. The VGG16(retrained on the dataset) model surpasses other ANN, CNN, TL models for multi-class tumor classification. This proposed network achieves significantly better performance with a validation accuracy of 94% and an F1-Score of 91. Keywords: Artificial Neural Network(ANN), Convolution Neural Network (CNN), Transfer Learning(TL), Magnetic Resonance Imaging(MRI.)

scholarly journals Development of brain tumor segmentation of magnetic resonance imaging (MRI) using U-Net deep learning

2021 ◽  
Vol 4 (9(112)) ◽  
pp. 23-31
Author(s):  
Wasan M. Jwaid ◽  
Zainab Shaker Matar Al-Husseini ◽  
Ahmad H. Sabry
Keyword(s):  
Magnetic Resonance Imaging ◽  
Deep Learning ◽  
Brain Tumor ◽  
Magnetic Resonance ◽  
Tumor Segmentation ◽  
Resonance Imaging ◽  
Brain Tumor Segmentation ◽  
Brain Images ◽  
Magnetic Resonance Imaging Mri ◽  
The Brain

Brain tumors are the growth of abnormal cells or a mass in a brain. Numerous kinds of brain tumors were discovered, which need accurate and early detection techniques. Currently, most diagnosis and detection methods rely on the decision of neuro-specialists and radiologists to evaluate brain images, which may be time-consuming and cause human errors. This paper proposes a robust U-Net deep learning Convolutional Neural Network (CNN) model that can classify if the subject has a tumor or not based on Brain Magnetic resonance imaging (MRI) with acceptable accuracy for medical-grade application. The study built and trained the 3D U-Net CNN including encoding/decoding relationship architecture to perform the brain tumor segmentation because it requires fewer training images and provides more precise segmentation. The algorithm consists of three parts; the first part, the downsampling part, the bottleneck part, and the optimum part. The resultant semantic maps are inserted into the decoder fraction to obtain the full-resolution probability maps. The developed U-Net architecture has been applied on the MRI scan brain tumor segmentation dataset in MICCAI BraTS 2017. The results using Matlab-based toolbox indicate that the proposed architecture has been successfully evaluated and experienced for MRI datasets of brain tumor segmentation including 336 images as training data and 125 images for validation. This work demonstrated comparative performance and successful feasibility of implementing U-Net CNN architecture in an automated framework of brain tumor segmentations in Fluid-attenuated inversion recovery (FLAIR) MR Slices. The developed U-Net CNN model succeeded in performing the brain tumor segmentation task to classify the input brain images into a tumor or not based on the MRI dataset.

scholarly journals Using deep learning to predict temporomandibular joint disc perforation based on magnetic resonance imaging

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jae-Young Kim ◽  
Dongwook Kim ◽  
Kug Jin Jeon ◽  
Hwiyoung Kim ◽  
Jong-Ki Huh
Keyword(s):  
Magnetic Resonance Imaging ◽  
Deep Learning ◽  
Magnetic Resonance ◽  
Random Forest ◽  
Temporomandibular Joint ◽  
Prediction Models ◽  
Superior Performance ◽  
Resonance Imaging ◽  
Temporomandibular Joint Disc ◽  
Magnetic Resonance Imaging Mri

AbstractThe goal of this study was to develop a deep learning-based algorithm to predict temporomandibular joint (TMJ) disc perforation based on the findings of magnetic resonance imaging (MRI) and to validate its performance through comparison with previously reported results. The study objects were obtained by reviewing medical records from January 2005 to June 2018. 299 joints from 289 patients were divided into perforated and non-perforated groups based on the existence of disc perforation confirmed during surgery. Experienced observers interpreted the TMJ MRI images to extract features. Data containing those features were applied to build and validate prediction models using random forest and multilayer perceptron (MLP) techniques, the latter using the Keras framework, a recent deep learning architecture. The area under the receiver operating characteristic (ROC) curve (AUC) was used to compare the performances of the models. MLP produced the best performance (AUC 0.940), followed by random forest (AUC 0.918) and disc shape alone (AUC 0.791). The MLP and random forest were also superior to previously reported results using MRI (AUC 0.808) and MRI-based nomogram (AUC 0.889). Implementing deep learning showed superior performance in predicting disc perforation in TMJ compared to conventional methods and previous reports.

scholarly journals Segmentasi Tumor Otak Berdasarkan Citra Magnetic Resonance Imaging Dengan Menggunakan Metode U-NET

2020 ◽  
Vol 19 (2) ◽  
pp. 151
Author(s):  
Ida Bagus Leo Mahadya Suta ◽  
Made Sudarma ◽  
I Nyoman Satya Kumara
Keyword(s):  
Magnetic Resonance Imaging ◽  
Deep Learning ◽  
Magnetic Resonance ◽  
Learning Rate ◽  
Batch Size ◽  
Resonance Imaging ◽  
Dice Coefficient ◽  
Magnetic Resonance Imaging Mri

Tumor otak merupakan salah satu penyakit yang mematikan dimana 3.7% per 100.000 pasien mengidap tumor ganas. Untuk menganalisa tumor otak dapat dilakukan melalui segmentasi citra Magnetic Resonance Imaging (MRI). Proses analisa citra secara otomatis dibutuhkan untuk menghemat waktu dan meningkatkan akurasi dari diagnosa yang dilakukan. Segmentasi secara otomatis dapat dilakukan dengan deep learning. U-NET merupakan salah satu metode yang digunakan untuk melakukan segmentasi citra medis karena bekerja dapa pixel level. Dengan menerapkan fungsi aktivasi ReLU dan Adam Optimizer, metode ini dapat menyelesaikan permasalahan segmentasi tumor otak. Dataset untuk proses training dan validation menggunakan BRATS 2017. Beberapa hyperparameter diterapkan pada metode ini yaitu, learning rate (lr) = 0.0001, batch size (bz) = 5, epoch = 80 dan beta (  ) = 0.9. Dari serangkaian proses yang dilakukan, akurasi metode U-NET dihitung dengan rumus Dice Coefficient dan menghasilkan nilai akurasi sebagai berikut: 90.22% (Full Tumor), 78.09% (Core Tumor) dan 80.20% (Enhancing Tumor).

scholarly journals Deep learning model for glioma, meningioma and pituitary classification

2021 ◽  
Vol 10 (1) ◽  
pp. 88
Author(s):  
Toqa A. Sadoon ◽  
Mohammed H. Ali
Keyword(s):  
Magnetic Resonance Imaging ◽  
Deep Learning ◽  
Brain Tumor ◽  
Magnetic Resonance ◽  
Resonance Imaging ◽  
Contrast Enhanced ◽  
Common Causes ◽  
The Difference ◽  
Magnetic Resonance Imaging Mri ◽  
Confusion Matrices

<p>One of the common causes of death is a brain tumor. Because of the above mentioned, early detection of a brain tumor is critical for faster treatment, and therefore there are many techniques used to visualize a brain tumor. One of these techniques is magnetic resonance imaging (MRI). On the other hand, machine learning, deep learning, and convolutional neural network (CNN) are the state of art technologies in the recent years used in solving many medical image-related problems such as classification. In this research, three types of brain tumors were classified using magnetic resonance imaging namely glioma, meningioma, and pituitary gland on the based of CNN. The dataset used in this work includes 233 patients for a total of 3,064 contrast-enhanced T1 images. In this paper, a comparison is presented between the presented model and other models to demonstrate the superiority of our model over the others. Moreover, the difference in outcome between pre- and post-data preprocessing and augmentation was discussed. The highest accuracy metrics extracted from confusion matrices are; precision of 99.1% for pituitary, sensitivity of 98.7% for glioma, specificity of 99.1%, and accuracy of 99.1% for pituitary. The overall accuracy obtained is 96.1%.</p>

scholarly journals A maChine and deep Learning Approach to predict pulmoNary hyperteNsIon in newbornS with congenital diaphragmatic Hernia (CLANNISH): Protocol for a retrospective study

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259724
Author(s):  
Ilaria Amodeo ◽  
Giorgio De Nunzio ◽  
Genny Raffaeli ◽  
Irene Borzani ◽  
Alice Griggio ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Pulmonary Hypertension ◽  
Deep Learning ◽  
Retrospective Study ◽  
Magnetic Resonance ◽  
Congenital Diaphragmatic Hernia ◽  
Diaphragmatic Hernia ◽  
Lung Volume ◽  
Resonance Imaging ◽  
Magnetic Resonance Imaging Mri

Introduction Outcome predictions of patients with congenital diaphragmatic hernia (CDH) still have some limitations in the prenatal estimate of postnatal pulmonary hypertension (PH). We propose applying Machine Learning (ML), and Deep Learning (DL) approaches to fetuses and newborns with CDH to develop forecasting models in prenatal epoch, based on the integrated analysis of clinical data, to provide neonatal PH as the first outcome and, possibly: favorable response to fetal endoscopic tracheal occlusion (FETO), need for Extracorporeal Membrane Oxygenation (ECMO), survival to ECMO, and death. Moreover, we plan to produce a (semi)automatic fetus lung segmentation system in Magnetic Resonance Imaging (MRI), which will be useful during project implementation but will also be an important tool itself to standardize lung volume measures for CDH fetuses. Methods and analytics Patients with isolated CDH from singleton pregnancies will be enrolled, whose prenatal checks were performed at the Fetal Surgery Unit of the Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico (Milan, Italy) from the 30th week of gestation. A retrospective data collection of clinical and radiological variables from newborns’ and mothers’ clinical records will be performed for eligible patients born between 01/01/2012 and 31/12/2020. The native sequences from fetal magnetic resonance imaging (MRI) will be collected. Data from different sources will be integrated and analyzed using ML and DL, and forecasting algorithms will be developed for each outcome. Methods of data augmentation and dimensionality reduction (feature selection and extraction) will be employed to increase sample size and avoid overfitting. A software system for automatic fetal lung volume segmentation in MRI based on the DL 3D U-NET approach will also be developed. Ethics and dissemination This retrospective study received approval from the local ethics committee (Milan Area 2, Italy). The development of predictive models in CDH outcomes will provide a key contribution in disease prediction, early targeted interventions, and personalized management, with an overall improvement in care quality, resource allocation, healthcare, and family savings. Our findings will be validated in a future prospective multicenter cohort study. Registration The study was registered at ClinicalTrials.gov with the identifier NCT04609163.

scholarly journals Improving Quantitative Magnetic Resonance Imaging Using Deep Learning

2020 ◽  
Vol 24 (04) ◽  
pp. 451-459
Author(s):  
Fang Liu
Keyword(s):  
Magnetic Resonance Imaging ◽  
Deep Learning ◽  
Magnetic Resonance ◽  
Quantitative Mri ◽  
Resonance Imaging ◽  
Tissue Segmentation ◽  
Learning Methods ◽  
Musculoskeletal Tissue ◽  
Conventional Machine ◽  
Magnetic Resonance Imaging Mri

AbstractDeep learning methods have shown promising results for accelerating quantitative musculoskeletal (MSK) magnetic resonance imaging (MRI) for T2 and T1ρ relaxometry. These methods have been shown to improve musculoskeletal tissue segmentation on parametric maps, allowing efficient and accurate T2 and T1ρ relaxometry analysis for monitoring and predicting MSK diseases. Deep learning methods have shown promising results for disease detection on quantitative MRI with diagnostic performance superior to conventional machine-learning methods for identifying knee osteoarthritis.

scholarly journals Deep Learning Approach in Brain Tumor Classification

2021 ◽  
pp. 246-250
Author(s):  
Bhavani Sankar A ◽  
Suryavarshini K
Keyword(s):  
Magnetic Resonance Imaging ◽  
Machine Learning ◽  
Deep Learning ◽  
Brain Tumor ◽  
Magnetic Resonance ◽  
Current Trend ◽  
Ultrasound Image ◽  
Tumor Classification ◽  
Resonance Imaging ◽  
Magnetic Resonance Imaging Mri

Various Computer-Aided Diagnosis (CAD) systems have been recently used in medical imaging to assist radiologist about their patients. Generally, various image technique such as Computer Tomography (CT), Magnetic Resonance Imaging (MRI) and ultrasound image are used to evaluate the tumor in a brain, lung, liver, breast, prostate etc., Especially, in this work MRI images are used to diagnose tumor in the brain. For full assistance of radiologists and better analysis of Magnetic Resonance Imaging, classification of brain tumor is essential procedure. The automatic classification scheme is essential to prevent the death rate of human. Deep learning is the newest and the current trend of machine learning field that paid a lot of the researchers’ attention in the recent few years. As a proven powerful machine learning tool, deep learning was widely used in several applications for solving various complex problems that require extremely high accuracy and sensitivity, particularly in the medical field. Tumor regions from an MR images are segmented using a deep learning technique. The automatic brain tumor classification is very challenging task in large spatial and structural variability of surrounding region of brain tumor. In this work, automatic brain tumor detection using Convolutional Neural Networks (CNN) classification. In general, brain tumor is one of the most common and aggressive malignant tumor diseases which is leading to very short expected life if it is diagnosed at higher grade. The deeper architecture design is performed by using small kernels. Other performance measures used in this study are the accuracy, sensitivity and specificity.

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