scholarly journals 3DMSNET: 3D CNN Based Brain MRI Segmentation

Segmentation of the brain images has become an important task to analyze the abnormality in infants. Automatic methods are important as the infant brain growth has to be tracked and it is almost impossible for an individual to manually segment the MRI data on particular intervals. The manual segmentation tasks are time-consuming and require highly skilled professionals to segment images. Automatic segmentation methods have gained huge support for segmenting MRI images. Several segmentation methods lack accuracies due to nearest neighbor or self-similarity problems. The CNNs have outperformed the traditional methods and are proving to be more reliable day by day. The proposed method is a patch-based method which uses 3DMSnet (3D Multi-Scale Network) for segmentation. The model is evaluated on BrainWeb and other publicly available datasets.

Author(s):  
Fatma Taher ◽  
Neema Prakash

Cerebrovascular diseases are one of the serious causes for the increase in mortality rate in the world which affect the blood vessels and blood supply to the brain. In order, diagnose and study the abnormalities in the cerebrovascular system, accurate segmentation methods can be used. The shape, direction and distribution of blood vessels can be studied using automatic segmentation. This will help the doctors to envisage the cerebrovascular system. Due to the complex shape and topology, automatic segmentation is still a challenge to the clinicians. In this paper, some of the latest approaches used for segmentation of magnetic resonance angiography images are explained. Some of such methods are deep convolutional neural network (CNN), 3dimentional-CNN (3D-CNN) and 3D U-Net. Finally, these methods are compared for evaluating their performance. 3D U-Net is the better performer among the described methods.


2014 ◽  
Author(s):  
Christian Wachinger ◽  
Matthew Brennan ◽  
Greg Sharp ◽  
Polina Golland

The segmentation of parotid glands in CT scans of patients with head and neck cancer is an essential part of treatment planning. We introduce a new method for the automatic segmentation of parotid glands that extends existing patch-based approaches in three ways: (1) we promote the use of image features in combination with patch intensity values to increase discrimination; (2) we work with larger search windows than established methods by using an approximate nearest neighbor search; and (3) we demonstrate that location information is a crucial discriminator and add it explicitly to the description. In our experiments, we compare a large number of features and introduce a new multi-scale descriptor. The best performance is achieved with entropy image features in combination with patches and location information.


2021 ◽  
Vol 11 (7) ◽  
pp. 629
Author(s):  
Bingjiang Qiu ◽  
Hylke van der Wel ◽  
Joep Kraeima ◽  
Haye Hendrik Glas ◽  
Jiapan Guo ◽  
...  

Medical imaging techniques, such as (cone beam) computed tomography and magnetic resonance imaging, have proven to be a valuable component for oral and maxillofacial surgery (OMFS). Accurate segmentation of the mandible from head and neck (H&N) scans is an important step in order to build a personalized 3D digital mandible model for 3D printing and treatment planning of OMFS. Segmented mandible structures are used to effectively visualize the mandible volumes and to evaluate particular mandible properties quantitatively. However, mandible segmentation is always challenging for both clinicians and researchers, due to complex structures and higher attenuation materials, such as teeth (filling) or metal implants that easily lead to high noise and strong artifacts during scanning. Moreover, the size and shape of the mandible vary to a large extent between individuals. Therefore, mandible segmentation is a tedious and time-consuming task and requires adequate training to be performed properly. With the advancement of computer vision approaches, researchers have developed several algorithms to automatically segment the mandible during the last two decades. The objective of this review was to present the available fully (semi)automatic segmentation methods of the mandible published in different scientific articles. This review provides a vivid description of the scientific advancements to clinicians and researchers in this field to help develop novel automatic methods for clinical applications.


Sensors ◽  
2021 ◽  
Vol 21 (10) ◽  
pp. 3363
Author(s):  
Chaitra Dayananda ◽  
Jae-Young Choi ◽  
Bumshik Lee

In this paper, we propose a multi-scale feature extraction with novel attention-based convolutional learning using the U-SegNet architecture to achieve segmentation of brain tissue from a magnetic resonance image (MRI). Although convolutional neural networks (CNNs) show enormous growth in medical image segmentation, there are some drawbacks with the conventional CNN models. In particular, the conventional use of encoder-decoder approaches leads to the extraction of similar low-level features multiple times, causing redundant use of information. Moreover, due to inefficient modeling of long-range dependencies, each semantic class is likely to be associated with non-accurate discriminative feature representations, resulting in low accuracy of segmentation. The proposed global attention module refines the feature extraction and improves the representational power of the convolutional neural network. Moreover, the attention-based multi-scale fusion strategy can integrate local features with their corresponding global dependencies. The integration of fire modules in both the encoder and decoder paths can significantly reduce the computational complexity owing to fewer model parameters. The proposed method was evaluated on publicly accessible datasets for brain tissue segmentation. The experimental results show that our proposed model achieves segmentation accuracies of 94.81% for cerebrospinal fluid (CSF), 95.54% for gray matter (GM), and 96.33% for white matter (WM) with a noticeably reduced number of learnable parameters. Our study shows better segmentation performance, improving the prediction accuracy by 2.5% in terms of dice similarity index while achieving a 4.5 times reduction in the number of learnable parameters compared to previously developed U-SegNet based segmentation approaches. This demonstrates that the proposed approach can achieve reliable and precise automatic segmentation of brain MRI images.


2011 ◽  
Vol 26 (S2) ◽  
pp. 914-914
Author(s):  
R. Barteček ◽  
N.E.M. van Haren ◽  
P.C.M.P. Koolschijn ◽  
H.E. Hulshoff Pol ◽  
R.S. Kahn

IntroductionPsychiatric Patients show abnormalities in volumes of several subcortical structures. Recently wider usage of automated segmentation methods in research of these abnormalities based on MR images has become possible. However manual segmentation is still considered to be the gold standard.ObjectivesTo compare differences in hippocampus volumes between manual segmentation and 2 packages for automatic segmentation (FSL and FreeSurfer).AimTo explore the overlap and differences between different segmentation methods used for segmentation of subcortical structures.MethodsStructural MR brain scans were aquired from 98 subjects (53 schizophrenia patients, 45 controls). Volumes of left and right hippocampus were measured after manual, FreeSurfer and FSL segmentations. Differences between volumes from different methods were tested by the t-test (using R). In addition percent volume differences, Pearson correlations, Bland-Altman plots and Cronbach’s alpha were computed.ResultsBoth automatic methods yielded significantly larger hippocampal volumes than the manual segmentation. FreeSurfer volumes showed a higher correlation and lower percent volume difference with manual segmentation than FSL. Bland-Altman plots and Cronbach’s alpha showed only limited agreement between manual and both automatic methods.ConclusionsAlthough volumes acquired by FreeSurfer appeared to be more related to manual segmentation, clear superiority of either of automatic methods could not be demonstrated. Therefore, all three methods seem to measure other aspects of hippocampus volume. An useful approach would be to compare effect-size of the difference between patients and healthy controls using different segmentation methods. We are currently pursuing this in a larger sample.


Author(s):  
Nidhal Khdhair El abbadi ◽  
Zahraa Faisal Shoman

Brain tumor is one of more dangerous diesis that affected more than 100 persons every day. The challenge is how to detect and recognise benign and malignant tumor without surgery. In this paper, initially, brain images are filtered to remove unwanted particles, then a new method for automatic segmentation of lesion area is carried out based on mean and standard deviation. Combining both solidity property and morphological operation used to detect only the tumor from segmented image. Mathematical morphology such as close used to join narrow breaks regions in an object, fill the small holes and remove small objects. Features extracted from image by using wavelet transform, followed by applying principle component analysis (PCA) to reduce the dimensions of features. Classification of tumor based on neural network, where the inputs to the network are thirteen statistical features and textural features. The algorithm is trained with 20 of brain MRI images and tested with 45 brain MRI images. Accuracy for this method was encourage and reach near 100% in identifying normal and abnormal tissues from MRI images.


Author(s):  
Ghazanfar Latif ◽  
Jaafar Alghazo ◽  
Fadi N. Sibai ◽  
D.N.F. Awang Iskandar ◽  
Adil H. Khan

Background: Variations of image segmentation techniques, particularly those used for Brain MRI segmentation, vary in complexity from basic standard Fuzzy C-means (FCM) to more complex and enhanced FCM techniques. Objective: In this paper, a comprehensive review is presented on all thirteen variations of FCM segmentation techniques. In the review process, the concentration is on the use of FCM segmentation techniques for brain tumors. Brain tumor segmentation is a vital step in the process of automatically diagnosing brain tumors. Unlike segmentation of other types of images, brain tumor segmentation is a very challenging task due to the variations in brain anatomy. The low contrast of brain images further complicates this process. Early diagnosis of brain tumors is indeed beneficial to patients, doctors, and medical providers. Results: FCM segmentation works on images obtained from magnetic resonance imaging (MRI) scanners, requiring minor modifications to hospital operations to early diagnose tumors as most, if not all, hospitals rely on MRI machines for brain imaging. In this paper, we critically review and summarize FCM based techniques for brain MRI segmentation.


2020 ◽  
Vol 961 (7) ◽  
pp. 47-55
Author(s):  
A.G. Yunusov ◽  
A.J. Jdeed ◽  
N.S. Begliarov ◽  
M.A. Elshewy

Laser scanning is considered as one of the most useful and fast technologies for modelling. On the other hand, the size of scan results can vary from hundreds to several million points. As a result, the large volume of the obtained clouds leads to complication at processing the results and increases the time costs. One way to reduce the volume of a point cloud is segmentation, which reduces the amount of data from several million points to a limited number of segments. In this article, we evaluated effect on the performance, the accuracy of various segmentation methods and the geometric accuracy of the obtained models at density changes taking into account the processing time. The results of our experiment were compared with reference data in a form of comparative analysis. As a conclusion, some recommendations for choosing the best segmentation method were proposed.


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