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Improving Patch-Based Convolutional Neural Networks for MRI Brain Tumor Segmentation by Leveraging Location Information.
The manual brain tumor annotation process is time consuming and resource consuming, therefore, an automated and accurate brain tumor segmentation tool is greatly in demand. In this paper, we introduce a novel method to integrate location information with the state-of-the-art patch-based neural networks for brain tumor segmentation. This is motivated by the observation that lesions are not uniformly distributed across different brain parcellation regions and that a locality-sensitive segmentation is likely to obtain better segmentation accuracy. Toward this, we use an existing brain parcellation atlas in the Montreal Neurological Institute (MNI) space and map this atlas to the individual subject data. This mapped atlas in the subject data space is integrated with structural Magnetic Resonance (MR) imaging data, and patch-based neural networks, including 3D U-Net and DeepMedic, are trained to classify the different brain lesions. Multiple state-of-the-art neural networks are trained and integrated with XGBoost fusion in the proposed two-level ensemble method. The first level reduces the uncertainty of the same type of models with different seed initializations, and the second level leverages the advantages of different types of neural network models. The proposed location information fusion method improves the segmentation performance of state-of-the-art networks including 3D U-Net and DeepMedic. Our proposed ensemble also achieves better segmentation performance compared to the state-of-the-art networks in BraTS 2017 and rivals state-of-the-art networks in BraTS 2018. Detailed results are provided on the public multimodal brain tumor segmentation (BraTS) benchmarks
A Deep Learning Framework for Unsupervised Affine and Deformable Image Registration
Image registration, the process of aligning two or more images, is the core
technique of many (semi-)automatic medical image analysis tasks. Recent studies
have shown that deep learning methods, notably convolutional neural networks
(ConvNets), can be used for image registration. Thus far training of ConvNets
for registration was supervised using predefined example registrations.
However, obtaining example registrations is not trivial. To circumvent the need
for predefined examples, and thereby to increase convenience of training
ConvNets for image registration, we propose the Deep Learning Image
Registration (DLIR) framework for \textit{unsupervised} affine and deformable
image registration. In the DLIR framework ConvNets are trained for image
registration by exploiting image similarity analogous to conventional
intensity-based image registration. After a ConvNet has been trained with the
DLIR framework, it can be used to register pairs of unseen images in one shot.
We propose flexible ConvNets designs for affine image registration and for
deformable image registration. By stacking multiple of these ConvNets into a
larger architecture, we are able to perform coarse-to-fine image registration.
We show for registration of cardiac cine MRI and registration of chest CT that
performance of the DLIR framework is comparable to conventional image
registration while being several orders of magnitude faster.Comment: Accepted: Medical Image Analysis - Elsevie
Shakeout: A New Approach to Regularized Deep Neural Network Training
Recent years have witnessed the success of deep neural networks in dealing
with a plenty of practical problems. Dropout has played an essential role in
many successful deep neural networks, by inducing regularization in the model
training. In this paper, we present a new regularized training approach:
Shakeout. Instead of randomly discarding units as Dropout does at the training
stage, Shakeout randomly chooses to enhance or reverse each unit's contribution
to the next layer. This minor modification of Dropout has the statistical
trait: the regularizer induced by Shakeout adaptively combines , and
regularization terms. Our classification experiments with representative
deep architectures on image datasets MNIST, CIFAR-10 and ImageNet show that
Shakeout deals with over-fitting effectively and outperforms Dropout. We
empirically demonstrate that Shakeout leads to sparser weights under both
unsupervised and supervised settings. Shakeout also leads to the grouping
effect of the input units in a layer. Considering the weights in reflecting the
importance of connections, Shakeout is superior to Dropout, which is valuable
for the deep model compression. Moreover, we demonstrate that Shakeout can
effectively reduce the instability of the training process of the deep
architecture.Comment: Appears at T-PAMI 201
Brain Tumor Segmentation and Tractographic Feature Extraction from Structural MR Images for Overall Survival Prediction
This paper introduces a novel methodology to integrate human brain
connectomics and parcellation for brain tumor segmentation and survival
prediction. For segmentation, we utilize an existing brain parcellation atlas
in the MNI152 1mm space and map this parcellation to each individual subject
data. We use deep neural network architectures together with hard negative
mining to achieve the final voxel level classification. For survival
prediction, we present a new method for combining features from connectomics
data, brain parcellation information, and the brain tumor mask. We leverage the
average connectome information from the Human Connectome Project and map each
subject brain volume onto this common connectome space. From this, we compute
tractographic features that describe potential neural disruptions due to the
brain tumor. These features are then used to predict the overall survival of
the subjects. The main novelty in the proposed methods is the use of normalized
brain parcellation data and tractography data from the human connectome project
for analyzing MR images for segmentation and survival prediction. Experimental
results are reported on the BraTS2018 dataset.Comment: 14 pages, 5 figures, 4 tables, accepted by BrainLes 2018 MICCAI
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