26,051 research outputs found
Automated Detection of Regions of Interest for Brain Perfusion MR Images
Images with abnormal brain anatomy produce problems for automatic
segmentation techniques, and as a result poor ROI detection affects both
quantitative measurements and visual assessment of perfusion data. This paper
presents a new approach for fully automated and relatively accurate ROI
detection from dynamic susceptibility contrast perfusion magnetic resonance and
can therefore be applied excellently in the perfusion analysis. In the proposed
approach the segmentation output is a binary mask of perfusion ROI that has
zero values for air pixels, pixels that represent non-brain tissues, and
cerebrospinal fluid pixels. The process of binary mask producing starts with
extracting low intensity pixels by thresholding. Optimal low-threshold value is
solved by obtaining intensity pixels information from the approximate
anatomical brain location. Holes filling algorithm and binary region growing
algorithm are used to remove falsely detected regions and produce region of
only brain tissues. Further, CSF pixels extraction is provided by thresholding
of high intensity pixels from region of only brain tissues. Each time-point
image of the perfusion sequence is used for adjustment of CSF pixels location.
The segmentation results were compared with the manual segmentation performed
by experienced radiologists, considered as the reference standard for
evaluation of proposed approach. On average of 120 images the segmentation
results have a good agreement with the reference standard. All detected
perfusion ROIs were deemed by two experienced radiologists as satisfactory
enough for clinical use. The results show that proposed approach is suitable to
be used for perfusion ROI detection from DSC head scans. Segmentation tool
based on the proposed approach can be implemented as a part of any automatic
brain image processing system for clinical use
Deep Neural Network with l2-norm Unit for Brain Lesions Detection
Automated brain lesions detection is an important and very challenging
clinical diagnostic task because the lesions have different sizes, shapes,
contrasts, and locations. Deep Learning recently has shown promising progress
in many application fields, which motivates us to apply this technology for
such important problem. In this paper, we propose a novel and end-to-end
trainable approach for brain lesions classification and detection by using deep
Convolutional Neural Network (CNN). In order to investigate the applicability,
we applied our approach on several brain diseases including high and low-grade
glioma tumor, ischemic stroke, Alzheimer diseases, by which the brain Magnetic
Resonance Images (MRI) have been applied as an input for the analysis. We
proposed a new operating unit which receives features from several projections
of a subset units of the bottom layer and computes a normalized l2-norm for
next layer. We evaluated the proposed approach on two different CNN
architectures and number of popular benchmark datasets. The experimental
results demonstrate the superior ability of the proposed approach.Comment: Accepted for presentation in ICONIP-201
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
Tversky loss function for image segmentation using 3D fully convolutional deep networks
Fully convolutional deep neural networks carry out excellent potential for
fast and accurate image segmentation. One of the main challenges in training
these networks is data imbalance, which is particularly problematic in medical
imaging applications such as lesion segmentation where the number of lesion
voxels is often much lower than the number of non-lesion voxels. Training with
unbalanced data can lead to predictions that are severely biased towards high
precision but low recall (sensitivity), which is undesired especially in
medical applications where false negatives are much less tolerable than false
positives. Several methods have been proposed to deal with this problem
including balanced sampling, two step training, sample re-weighting, and
similarity loss functions. In this paper, we propose a generalized loss
function based on the Tversky index to address the issue of data imbalance and
achieve much better trade-off between precision and recall in training 3D fully
convolutional deep neural networks. Experimental results in multiple sclerosis
lesion segmentation on magnetic resonance images show improved F2 score, Dice
coefficient, and the area under the precision-recall curve in test data. Based
on these results we suggest Tversky loss function as a generalized framework to
effectively train deep neural networks
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