276 research outputs found
Scalable multimodal convolutional networks for brain tumour segmentation
Brain tumour segmentation plays a key role in computer-assisted surgery. Deep
neural networks have increased the accuracy of automatic segmentation
significantly, however these models tend to generalise poorly to different
imaging modalities than those for which they have been designed, thereby
limiting their applications. For example, a network architecture initially
designed for brain parcellation of monomodal T1 MRI can not be easily
translated into an efficient tumour segmentation network that jointly utilises
T1, T1c, Flair and T2 MRI. To tackle this, we propose a novel scalable
multimodal deep learning architecture using new nested structures that
explicitly leverage deep features within or across modalities. This aims at
making the early layers of the architecture structured and sparse so that the
final architecture becomes scalable to the number of modalities. We evaluate
the scalable architecture for brain tumour segmentation and give evidence of
its regularisation effect compared to the conventional concatenation approach.Comment: Paper accepted at MICCAI 201
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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
Automatic Brain Tumor Segmentation using Cascaded Anisotropic Convolutional Neural Networks
A cascade of fully convolutional neural networks is proposed to segment
multi-modal Magnetic Resonance (MR) images with brain tumor into background and
three hierarchical regions: whole tumor, tumor core and enhancing tumor core.
The cascade is designed to decompose the multi-class segmentation problem into
a sequence of three binary segmentation problems according to the subregion
hierarchy. The whole tumor is segmented in the first step and the bounding box
of the result is used for the tumor core segmentation in the second step. The
enhancing tumor core is then segmented based on the bounding box of the tumor
core segmentation result. Our networks consist of multiple layers of
anisotropic and dilated convolution filters, and they are combined with
multi-view fusion to reduce false positives. Residual connections and
multi-scale predictions are employed in these networks to boost the
segmentation performance. Experiments with BraTS 2017 validation set show that
the proposed method achieved average Dice scores of 0.7859, 0.9050, 0.8378 for
enhancing tumor core, whole tumor and tumor core, respectively. The
corresponding values for BraTS 2017 testing set were 0.7831, 0.8739, and
0.7748, respectively.Comment: 12 pages, 5 figures. MICCAI Brats Challenge 201
Automated brain tumour identification using magnetic resonance imaging:a systematic review and meta-analysis
BACKGROUND: Automated brain tumor identification facilitates diagnosis and treatment planning. We evaluate the performance of traditional machine learning (TML) and deep learning (DL) in brain tumor detection and segmentation, using MRI. METHODS: A systematic literature search from January 2000 to May 8, 2021 was conducted. Study quality was assessed using the Checklist for Artificial Intelligence in Medical Imaging (CLAIM). Detection meta-analysis was performed using a unified hierarchical model. Segmentation studies were evaluated using a random effects model. Sensitivity analysis was performed for externally validated studies. RESULTS: Of 224 studies included in the systematic review, 46 segmentation and 38 detection studies were eligible for meta-analysis. In detection, DL achieved a lower false positive rate compared to TML; 0.018 (95% CI, 0.011 to 0.028) and 0.048 (0.032 to 0.072) (P < .001), respectively. In segmentation, DL had a higher dice similarity coefficient (DSC), particularly for tumor core (TC); 0.80 (0.77 to 0.83) and 0.63 (0.56 to 0.71) (P < .001), persisting on sensitivity analysis. Both manual and automated whole tumor (WT) segmentation had “good” (DSC ≥ 0.70) performance. Manual TC segmentation was superior to automated; 0.78 (0.69 to 0.86) and 0.64 (0.53 to 0.74) (P = .014), respectively. Only 30% of studies reported external validation. CONCLUSIONS: The comparable performance of automated to manual WT segmentation supports its integration into clinical practice. However, manual outperformance for sub-compartmental segmentation highlights the need for further development of automated methods in this area. Compared to TML, DL provided superior performance for detection and sub-compartmental segmentation. Improvements in the quality and design of studies, including external validation, are required for the interpretability and generalizability of automated models
Hetero-Modal Variational Encoder-Decoder for Joint Modality Completion and Segmentation
We propose a new deep learning method for tumour segmentation when dealing
with missing imaging modalities. Instead of producing one network for each
possible subset of observed modalities or using arithmetic operations to
combine feature maps, our hetero-modal variational 3D encoder-decoder
independently embeds all observed modalities into a shared latent
representation. Missing data and tumour segmentation can be then generated from
this embedding. In our scenario, the input is a random subset of modalities. We
demonstrate that the optimisation problem can be seen as a mixture sampling. In
addition to this, we introduce a new network architecture building upon both
the 3D U-Net and the Multi-Modal Variational Auto-Encoder (MVAE). Finally, we
evaluate our method on BraTS2018 using subsets of the imaging modalities as
input. Our model outperforms the current state-of-the-art method for dealing
with missing modalities and achieves similar performance to the subset-specific
equivalent networks.Comment: Accepted at MICCAI 201
Interactive Medical Image Segmentation using Deep Learning with Image-specific Fine-tuning
Convolutional neural networks (CNNs) have achieved state-of-the-art
performance for automatic medical image segmentation. However, they have not
demonstrated sufficiently accurate and robust results for clinical use. In
addition, they are limited by the lack of image-specific adaptation and the
lack of generalizability to previously unseen object classes. To address these
problems, we propose a novel deep learning-based framework for interactive
segmentation by incorporating CNNs into a bounding box and scribble-based
segmentation pipeline. We propose image-specific fine-tuning to make a CNN
model adaptive to a specific test image, which can be either unsupervised
(without additional user interactions) or supervised (with additional
scribbles). We also propose a weighted loss function considering network and
interaction-based uncertainty for the fine-tuning. We applied this framework to
two applications: 2D segmentation of multiple organs from fetal MR slices,
where only two types of these organs were annotated for training; and 3D
segmentation of brain tumor core (excluding edema) and whole brain tumor
(including edema) from different MR sequences, where only tumor cores in one MR
sequence were annotated for training. Experimental results show that 1) our
model is more robust to segment previously unseen objects than state-of-the-art
CNNs; 2) image-specific fine-tuning with the proposed weighted loss function
significantly improves segmentation accuracy; and 3) our method leads to
accurate results with fewer user interactions and less user time than
traditional interactive segmentation methods.Comment: 11 pages, 11 figure
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