Progressive multi-atlas label fusion by dictionary evolution

Anatomical Attention Guided Deep Networks for ROI Segmentation of Brain MR Images

Brain region-of-interest (ROI) segmentation based on structural magnetic resonance imaging (MRI) scans is an essential step for many computer-aid medical image analysis applications. Due to low intensity contrast around ROI boundary and large inter-subject variance, it has been remaining a challenging task to effectively segment brain ROIs from structural MR images. Even though several deep learning methods for brain MR image segmentation have been developed, most of them do not incorporate shape priors to take advantage of the regularity of brain structures, thus leading to sub-optimal performance. To address this issue, we propose an anatomical attention guided deep learning framework for brain ROI segmentation of structural MR images, containing two subnetworks. The first one is a segmentation subnetwork, used to simultaneously extract discriminative image representation and segment ROIs for each input MR image. The second one is an anatomical attention subnetwork, designed to capture the anatomical structure information of the brain from a set of labeled atlases. To utilize the anatomical attention knowledge learned from atlases, we develop an anatomical gate architecture to fuse feature maps derived from a set of atlas label maps and those from the to-be-segmented image for brain ROI segmentation. In this way, the anatomical prior learned from atlases can be explicitly employed to guide the segmentation process for performance improvement. Within this framework, we develop two anatomical attention guided segmentation models, denoted as anatomical gated fully convolutional network (AG-FCN) and anatomical gated U-Net (AG-UNet), respectively. Experimental results on both ADNI and LONI-LPBA40 datasets suggest that the proposed AG-FCN and AG-UNet methods achieve superior performance in ROI segmentation of brain MR images, compared with several state-of-the-art methods.

High-order Feature Learning for Multi-atlas based Label Fusion: Application to Brain Segmentation with MRI

Multi-atlas based segmentation methods have shown their effectiveness in brain regions-of-interesting (ROIs) segmentation, by propagating labels from multiple atlases to a target image based on the similarity between patches in the target image and multiple atlas images. Most of the existing multiatlas based methods use image intensity features to calculate the similarity between a pair of image patches for label fusion. In particular, using only low-level image intensity features cannot adequately characterize the complex appearance patterns (e.g., the high-order relationship between voxels within a patch) of brain magnetic resonance (MR) images. To address this issue, this paper develops a high-order feature learning framework for multi-atlas based label fusion, where high-order features of image patches are extracted and fused for segmenting ROIs of structural brain MR images. Specifically, an unsupervised feature learning method (i.e., means-covariances restricted Boltzmann machine, mcRBM) is employed to learn high-order features (i.e., mean and covariance features) of patches in brain MR images. Then, a group-fused sparsity dictionary learning method is proposed to jointly calculate the voting weights for label fusion, based on the learned high-order and the original image intensity features. The proposed method is compared with several state-of-the-art label fusion methods on ADNI, NIREP and LONI-LPBA40 datasets. The Dice ratio achieved by our method is 88:30%, 88:83%, 79:54% and 81:02% on left and right hippocampus on the ADNI, NIREP and LONI-LPBA40 datasets, respectively, while the best Dice ratio yielded by the other methods are 86:51%, 87:39%, 78:48% and 79:65% on three datasets, respectively.

Non-linear registration improves statistical power to detect hippocampal atrophy in aging and dementia

OBJECTIVE

To compare the performance of different methods for determining hippocampal atrophy rates using longitudinal MRI scans in aging and Alzheimer's disease (AD).

BACKGROUND

Quantifying hippocampal atrophy caused by neurodegenerative diseases is important to follow the course of the disease. In dementia, the efficacy of new therapies can be partially assessed by measuring their effect on hippocampal atrophy. In radiotherapy, the quantification of radiation-induced hippocampal volume loss is of interest to quantify radiation damage. We evaluated plausibility, reproducibility and sensitivity of eight commonly used methods to determine hippocampal atrophy rates using test-retest scans.

MATERIALS AND METHODS

Manual, FSL-FIRST, FreeSurfer, multi-atlas segmentation (MALF) and non-linear registration methods (Elastix, NiftyReg, ANTs and MIRTK) were used to determine hippocampal atrophy rates on longitudinal T1-weighted MRI from the ADNI database. Appropriate parameters for the non-linear registration methods were determined using a small training dataset (N = 16) in which two-year hippocampal atrophy was measured using test-retest scans of 8 subjects with low and 8 subjects with high atrophy rates. On a larger dataset of 20 controls, 40 mild cognitive impairment (MCI) and 20  AD patients, one-year hippocampal atrophy rates were measured. A repeated measures ANOVA analysis was performed to determine differences between controls, MCI and AD patients. For each method we calculated effect sizes and the required sample sizes to detect one-year volume change between controls and MCI (NCTRL_MCI) and between controls and AD (NCTRL_AD). Finally, reproducibility of hippocampal atrophy rates was assessed using within-session rescans and expressed as an average distance measure DAve, which expresses the difference in atrophy rate, averaged over all subjects. The same DAve was used to determine the agreement between different methods.

RESULTS

Except for MALF, all methods detected a significant group difference between CTRL and AD, but none could find a significant difference between the CTRL and MCI. FreeSurfer and MIRTK required the lowest sample sizes (FreeSurfer: NCTRL_MCI = 115, NCTRL_AD = 17 with DAve = 3.26%; MIRTK: NCTRL_MCI = 97, NCTRL_AD = 11 with DAve = 3.76%), while ANTs was most reproducible (NCTRL_MCI = 162, NCTRL_AD = 37 with DAve = 1.06%), followed by Elastix (NCTRL_MCI = 226, NCTRL_AD = 15 with DAve = 1.78%) and NiftyReg (NCTRL_MCI = 193, NCTRL_AD = 14 with DAve = 2.11%). Manually measured hippocampal atrophy rates required largest sample sizes to detect volume change and were poorly reproduced (NCTRL_MCI = 452, NCTRL_AD = 87 with DAve = 12.39%). Atrophy rates of non-linear registration methods also agreed best with each other.

DISCUSSION AND CONCLUSION

Non-linear registration methods were most consistent in determining hippocampal atrophy and because of their better reproducibility, methods, such as ANTs, Elastix and NiftyReg, are preferred for determining hippocampal atrophy rates on longitudinal MRI. Since performances of non-linear registration methods are well comparable, the preferred method would mostly depend on computational efficiency.

Adaptive Bayesian label fusion using kernel-based similarity metrics in hippocampus segmentation

The effectiveness of brain magnetic resonance imaging (MRI) as a useful evaluation tool strongly depends on the performed segmentation of associated tissues or anatomical structures. We introduce an enhanced brain segmentation approach of Bayesian label fusion that includes the construction of adaptive target-specific probabilistic priors using atlases ranked by kernel-based similarity metrics to deal with the anatomical variability of collected MRI data. In particular, the developed segmentation approach appraises patch-based voxel representation to enhance the voxel embedding in spaces with increased tissue discrimination, as well as the construction of a neighborhood-dependent model that addresses the label assignment of each region with a different patch complexity. To measure the similarity between the target and training atlases, we propose a tensor-based kernel metric that also includes the training labeling set. We evaluate the proposed approach, adaptive Bayesian label fusion using kernel-based similarity metrics, in the specific case of hippocampus segmentation of five benchmark MRI collections, including ADNI dataset, resulting in an increased performance (assessed through the Dice index) as compared to other recent works.

Accurate Pelvis and Femur Segmentation in Hip CT With a Novel Patch-Based Refinement

Due to bone deformation and joint space narrowing in diseased hips, accurate segmentation for pelvis, and femur from hip computed tomography (CT) images remains a challenging task. Therefore, the paper presents a fully automatic segmentation framework for the pelvis and femur in both of healthy and diseased hips. The framework involves three steps: preprocessing, coarse segmentation, and refinement. It starts with a preprocessing procedure to extract the volume of interest (VOI) from original CT images. Then, a coarse segmentation of bone has been obtained by classifying the VOI as bone and nonbone parts based on conditional random field (CRF) model. Finally, the bone is further divided into the pelvis and femur using a patch-based refinement method. The innovation of this study is the novel patch-based refinement method that is particularly suitable for diseased hips. The refinement method starts from the boundary of coarse segmentation, and propagates to the neighbors only when the label is not consistent with the label of CRF-based classification, it increases the reliability of segmentation for diseased hips with bone deformation. We incorporate neighborhood information to label fusion so that final label estimation is more accurate and robust for diseased hips with joint space narrowing. In total, 60 CT data sets, which included 78 healthy hemi-hips and 42 diseased hemi-hips, were used, and three-fold cross validations were carried out. Compared to two state-of-the-art methods, our method achieved significantly increased segmentation accuracy for the diseased hemi-hips, and is, therefore, more suited for automatic segmentation of diseased hips.