6,008 research outputs found
End-to-end learning of brain tissue segmentation from imperfect labeling
Segmenting a structural magnetic resonance imaging (MRI) scan is an important
pre-processing step for analytic procedures and subsequent inferences about
longitudinal tissue changes. Manual segmentation defines the current gold
standard in quality but is prohibitively expensive. Automatic approaches are
computationally intensive, incredibly slow at scale, and error prone due to
usually involving many potentially faulty intermediate steps. In order to
streamline the segmentation, we introduce a deep learning model that is based
on volumetric dilated convolutions, subsequently reducing both processing time
and errors. Compared to its competitors, the model has a reduced set of
parameters and thus is easier to train and much faster to execute. The contrast
in performance between the dilated network and its competitors becomes obvious
when both are tested on a large dataset of unprocessed human brain volumes. The
dilated network consistently outperforms not only another state-of-the-art deep
learning approach, the up convolutional network, but also the ground truth on
which it was trained. Not only can the incredible speed of our model make large
scale analyses much easier but we also believe it has great potential in a
clinical setting where, with little to no substantial delay, a patient and
provider can go over test results.Comment: Published as a conference paper at IJCNN 2017 Preprint versio
Automated hippocampal segmentation in patients with epilepsy: Available free online
Hippocampal sclerosis, a common cause of refractory focal epilepsy, requires hippocampal volumetry for accurate diagnosis and surgical planning. Manual segmentation is time-consuming and subject to interrater/intrarater variability. Automated algorithms perform poorly in patients with temporal lobe epilepsy. We validate and make freely available online a novel automated method
Sub-cortical brain structure segmentation using F-CNN's
In this paper we propose a deep learning approach for segmenting sub-cortical
structures of the human brain in Magnetic Resonance (MR) image data. We draw
inspiration from a state-of-the-art Fully-Convolutional Neural Network (F-CNN)
architecture for semantic segmentation of objects in natural images, and adapt
it to our task. Unlike previous CNN-based methods that operate on image
patches, our model is applied on a full blown 2D image, without any alignment
or registration steps at testing time. We further improve segmentation results
by interpreting the CNN output as potentials of a Markov Random Field (MRF),
whose topology corresponds to a volumetric grid. Alpha-expansion is used to
perform approximate inference imposing spatial volumetric homogeneity to the
CNN priors. We compare the performance of the proposed pipeline with a similar
system using Random Forest-based priors, as well as state-of-art segmentation
algorithms, and show promising results on two different brain MRI datasets.Comment: ISBI 2016: International Symposium on Biomedical Imaging, Apr 2016,
Prague, Czech Republi
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