3,354 research outputs found
Real-Time Automatic Fetal Brain Extraction in Fetal MRI by Deep Learning
Brain segmentation is a fundamental first step in neuroimage analysis. In the
case of fetal MRI, it is particularly challenging and important due to the
arbitrary orientation of the fetus, organs that surround the fetal head, and
intermittent fetal motion. Several promising methods have been proposed but are
limited in their performance in challenging cases and in real-time
segmentation. We aimed to develop a fully automatic segmentation method that
independently segments sections of the fetal brain in 2D fetal MRI slices in
real-time. To this end, we developed and evaluated a deep fully convolutional
neural network based on 2D U-net and autocontext, and compared it to two
alternative fast methods based on 1) a voxelwise fully convolutional network
and 2) a method based on SIFT features, random forest and conditional random
field. We trained the networks with manual brain masks on 250 stacks of
training images, and tested on 17 stacks of normal fetal brain images as well
as 18 stacks of extremely challenging cases based on extreme motion, noise, and
severely abnormal brain shape. Experimental results show that our U-net
approach outperformed the other methods and achieved average Dice metrics of
96.52% and 78.83% in the normal and challenging test sets, respectively. With
an unprecedented performance and a test run time of about 1 second, our network
can be used to segment the fetal brain in real-time while fetal MRI slices are
being acquired. This can enable real-time motion tracking, motion detection,
and 3D reconstruction of fetal brain MRI.Comment: This work has been submitted to ISBI 201
Fetal-BET: Brain Extraction Tool for Fetal MRI
Fetal brain extraction is a necessary first step in most computational fetal
brain MRI pipelines. However, it has been a very challenging task due to
non-standard fetal head pose, fetal movements during examination, and vastly
heterogeneous appearance of the developing fetal brain and the neighboring
fetal and maternal anatomy across various sequences and scanning conditions.
Development of a machine learning method to effectively address this task
requires a large and rich labeled dataset that has not been previously
available. As a result, there is currently no method for accurate fetal brain
extraction on various fetal MRI sequences. In this work, we first built a large
annotated dataset of approximately 72,000 2D fetal brain MRI images. Our
dataset covers the three common MRI sequences including T2-weighted,
diffusion-weighted, and functional MRI acquired with different scanners.
Moreover, it includes normal and pathological brains. Using this dataset, we
developed and validated deep learning methods, by exploiting the power of the
U-Net style architectures, the attention mechanism, multi-contrast feature
learning, and data augmentation for fast, accurate, and generalizable automatic
fetal brain extraction. Our approach leverages the rich information from
multi-contrast (multi-sequence) fetal MRI data, enabling precise delineation of
the fetal brain structures. Evaluations on independent test data show that our
method achieves accurate brain extraction on heterogeneous test data acquired
with different scanners, on pathological brains, and at various gestational
stages. This robustness underscores the potential utility of our deep learning
model for fetal brain imaging and image analysis.Comment: 10 pages, 6 figures, 2 TABLES, This work has been submitted to the
IEEE Transactions on Medical Imaging for possible publication. Copyright may
be transferred without notice, after which this version may no longer be
accessibl
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
Fully automated planning for anatomical fetal brain MRI on 0.55T
Purpose: Widening the availability of fetal MRI with fully automatic
real-time planning of radiological brain planes on 0.55T MRI. Methods: Deep
learning-based detection of key brain landmarks on a whole-uterus EPI scan
enables the subsequent fully automatic planning of the radiological single-shot
Turbo Spin Echo acquisitions. The landmark detection pipeline was trained on
over 120 datasets from varying field strength, echo times and resolutions and
quantitatively evaluated. The entire automatic planning solution was tested
prospectively in nine fetal subjects between 20 and 37 weeks. Comprehensive
evaluation of all steps, the distance between manual and automatic landmarks,
the planning quality and the resulting image quality was conducted. Results:
Prospective automatic planning was performed in real-time without latency in
all subjects. The landmark detection accuracy was 4.21+-2.56 mm for the fetal
eyes and 6.47+-3.23 for the cerebellum, planning quality was 2.44/3 (compared
to 2.56/3 for manual planning) and diagnostic image quality was 2.14 compared
to 2.07 for manual planning. Conclusions: Real-time automatic planning of all
three key fetal brain planes was successfully achieved and will pave the way
towards simplifying the acquisition of fetal MRI thereby widening the
availability of this modality in non-specialist centres.Comment: 17 pages, 8 figures, 1 table, MR
Segmentation of fetal 2D images with deep learning: a review
Image segmentation plays a vital role in
providing sustainable medical care in this evolving biomedical
image processing technology. Nowadays, it is considered one of
the most important research directions in the computer vision
field. Since the last decade, deep learning-based medical image
processing has become a research hotspot due to its exceptional
performance. In this paper, we present a review of different
deep learning techniques used to segment fetal 2D images.
First, we explain the basic ideas of each approach and then
thoroughly investigate the methods used for the segmentation
of fetal images. Secondly, the results and accuracy of different
approaches are also discussed. The dataset details used for
assessing the performance of the respective method are also
documented. Based on the review studies, the challenges and
future work are also pointed out at the end. As a result, it is
shown that deep learning techniques are very effective in the
segmentation of fetal 2D images.info:eu-repo/semantics/publishedVersio
Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images
We propose a novel attention gate (AG) model for medical image analysis that
automatically learns to focus on target structures of varying shapes and sizes.
Models trained with AGs implicitly learn to suppress irrelevant regions in an
input image while highlighting salient features useful for a specific task.
This enables us to eliminate the necessity of using explicit external
tissue/organ localisation modules when using convolutional neural networks
(CNNs). AGs can be easily integrated into standard CNN models such as VGG or
U-Net architectures with minimal computational overhead while increasing the
model sensitivity and prediction accuracy. The proposed AG models are evaluated
on a variety of tasks, including medical image classification and segmentation.
For classification, we demonstrate the use case of AGs in scan plane detection
for fetal ultrasound screening. We show that the proposed attention mechanism
can provide efficient object localisation while improving the overall
prediction performance by reducing false positives. For segmentation, the
proposed architecture is evaluated on two large 3D CT abdominal datasets with
manual annotations for multiple organs. Experimental results show that AG
models consistently improve the prediction performance of the base
architectures across different datasets and training sizes while preserving
computational efficiency. Moreover, AGs guide the model activations to be
focused around salient regions, which provides better insights into how model
predictions are made. The source code for the proposed AG models is publicly
available.Comment: Accepted for Medical Image Analysis (Special Issue on Medical Imaging
with Deep Learning). arXiv admin note: substantial text overlap with
arXiv:1804.03999, arXiv:1804.0533
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