16 research outputs found
TBI Contusion Segmentation from MRI using Convolutional Neural Networks
Traumatic brain injury (TBI) is caused by a sudden trauma to the head that
may result in hematomas and contusions and can lead to stroke or chronic
disability. An accurate quantification of the lesion volumes and their
locations is essential to understand the pathophysiology of TBI and its
progression. In this paper, we propose a fully convolutional neural network
(CNN) model to segment contusions and lesions from brain magnetic resonance
(MR) images of patients with TBI. The CNN architecture proposed here was based
on a state of the art CNN architecture from Google, called Inception. Using a
3-layer Inception network, lesions are segmented from multi-contrast MR images.
When compared with two recent TBI lesion segmentation methods, one based on CNN
(called DeepMedic) and another based on random forests, the proposed algorithm
showed improved segmentation accuracy on images of 18 patients with mild to
severe TBI. Using a leave-one-out cross validation, the proposed model achieved
a median Dice of 0.75, which was significantly better (p<0.01) than the two
competing methods.Comment: https://ieeexplore.ieee.org/abstract/document/8363545/, IEEE 15th
International Symposium on Biomedical Imaging (ISBI 2018
Temporal filtering of longitudinal brain magnetic resonance images for consistent segmentation
Longitudinal analysis of magnetic resonance images of the human brain provides knowledge of brain changes during both normal aging as well as the progression of many diseases. Previous longitudinal segmentation methods have either ignored temporal information or have incorporated temporal consistency constraints within the algorithm. In this work, we assume that some anatomical brain changes can be explained by temporal transitions in image intensities. Once the images are aligned in the same space, the intensities of each scan at the same voxel constitute a temporal (or 4D) intensity trend at that voxel. Temporal intensity variations due to noise or other artifacts are corrected by a 4D intensity-based filter that smooths the intensity values where appropriate, while preserving real anatomical changes such as atrophy. Here smoothing refers to removal of sudden changes or discontinuities in intensities. Images processed with the 4D filter can be used as a pre-processing step to any segmentation method. We show that such a longitudinal pre-processing step produces robust and consistent longitudinal segmentation results, even when applying 3D segmentation algorithms. We compare with state-of-the-art 4D segmentation algorithms. Specifically, we experimented on three longitudinal datasets containing 4–12 time-points, and showed that the 4D temporal filter is more robust and has more power in distinguishing between healthy subjects and those with dementia, mild cognitive impairment, as well as different phenotypes of multiple sclerosis
Longitudinal multiple sclerosis lesion segmentation data resource
The data presented in this article is related to the research article entitled “Longitudinal multiple sclerosis lesion segmentation: Resource and challenge” (Carass et al., 2017) [1]. In conjunction with the 2015 International Symposium on Biomedical Imaging, we organized a longitudinal multiple sclerosis (MS) lesion segmentation challenge providing training and test data to registered participants. The training data consists of five subjects with a mean of 4.4 (±0.55) time-points, and test data of fourteen subjects with a mean of 4.4 (±0.67) time-points. All 82 data sets had the white matter lesions associated with multiple sclerosis delineated by two human expert raters. The training data including multi-modal scans and manually delineated lesion masks is available for download. In addition, the testing data is also being made available in conjunction with a website for evaluating the automated analysis of the testing data