Deformable appearance pyramids for anatomy representation, landmark detection and pathology classification.
Ontology highlight
ABSTRACT:
SUBMITTER: Zhang Q
PROVIDER: S-EPMC5541155 | biostudies-other | 2017 Aug
REPOSITORIES: biostudies-other
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Project description:PurposeDeformable image registration (DIR) can benefit from additional guidance using corresponding landmarks in the images. However, the benefits thereof are largely understudied, especially due to the lack of automatic landmark detection methods for three-dimensional (3D) medical images.ApproachWe present a deep convolutional neural network (DCNN), called DCNN-Match, that learns to predict landmark correspondences in 3D images in a self-supervised manner. We trained DCNN-Match on pairs of computed tomography (CT) scans containing simulated deformations. We explored five variants of DCNN-Match that use different loss functions and assessed their effect on the spatial density of predicted landmarks and the associated matching errors. We also tested DCNN-Match variants in combination with the open-source registration software Elastix to assess the impact of predicted landmarks in providing additional guidance to DIR.ResultsWe tested our approach on lower abdominal CT scans from cervical cancer patients: 121 pairs containing simulated deformations and 11 pairs demonstrating clinical deformations. The results showed significant improvement in DIR performance when landmark correspondences predicted by DCNN-Match were used in the case of simulated ( p = 0 e 0 ) as well as clinical deformations ( p = 0.030 ). We also observed that the spatial density of the automatic landmarks with respect to the underlying deformation affect the extent of improvement in DIR. Finally, DCNN-Match was found to generalize to magnetic resonance imaging scans without requiring retraining, indicating easy applicability to other datasets.ConclusionsDCNN-match learns to predict landmark correspondences in 3D medical images in a self-supervised manner, which can improve DIR performance.
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Project description:US image registration is an important task e.g. in Computer Aided Surgery. Due to tissue deformation occurring between pre-operative and interventional images often deformable registration is necessary. We present a registration method focused on surface structures (i.e. saliencies) of soft tissues like organ capsules or vessels. The main concept follows the idea of representative landmarks (so called leading points). These landmarks represent saliencies in each image in a certain region of interest. The determination of deformation was based on a geometric model assuming that saliencies could locally be described by planes. These planes were calculated from the landmarks using two dimensional linear regression. Once corresponding regions in both images were found, a displacement vector field representing the local deformation was computed. Finally, the deformed image was warped to match the pre-operative image. For error calculation we used a phantom representing the urinary bladder and the prostate. The phantom could be deformed to mimic tissue deformation. Error calculation was done using corresponding landmarks in both images. The resulting target registration error of this procedure amounted to 1.63 mm. With respect to patient data a full deformable registration was performed on two 3D-US images of the abdomen. The resulting mean distance error was 2.10 ± 0.66 mm compared to an error of 2.75 ± 0.57 mm from a simple rigid registration. A two-sided paired t-test showed a p-value < 0.001. We conclude that the method improves the results of the rigid registration considerably. Provided an appropriate choice of the filter there are many possible fields of applications.
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Project description:PurposeDeformable image registration (DIR) is a key enabling technology in many diagnostic and therapeutic tasks, but often does not meet the required robustness and accuracy for supporting clinical tasks. This is in large part due to a lack of high-quality benchmark datasets by which new DIR algorithms can be evaluated. Our team was supported by the National Institute of Biomedical Imaging and Bioengineering to develop DIR benchmark dataset libraries for multiple anatomical sites, comprising of large numbers of highly accurate landmark pairs on matching blood vessel bifurcations. Here we introduce our lung CT DIR benchmark dataset library, which was developed to improve upon the number and distribution of landmark pairs in current public lung CT benchmark datasets.Acquisition and validation methodsThirty CT image pairs were acquired from several publicly available repositories as well as authors' institution with IRB approval. The data processing workflow included multiple steps: (1) The images were denoised. (2) Lungs, airways, and blood vessels were automatically segmented. (3) Bifurcations were directly detected on the skeleton of the segmented vessel tree. (4) Falsely identified bifurcations were filtered out using manually defined rules. (5) A DIR was used to project landmarks detected on the first image onto the second image of the image pair to form landmark pairs. (6) Landmark pairs were manually verified. This workflow resulted in an average of 1262 landmark pairs per image pair. Estimates of the landmark pair target registration error (TRE) using digital phantoms were 0.4 mm ± 0.3 mm.Data format and usage notesThe data is published in Zenodo at https://doi.org/10.5281/zenodo.8200423. Instructions for use can be found at https://github.com/deshanyang/Lung-DIR-QA.Potential applicationsThe dataset library generated in this work is the largest of its kind to date and will provide researchers with a new and improved set of ground truth benchmarks for quantitatively validating DIR algorithms within the lung.
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Project description:PurposeAnnotation of meaningful landmark ground truth on DCE-MRI is difficult and laborious. Motion correction methods applied to DCE-MRI of the liver are thus mostly evaluated using qualitative or indirect measures. We propose a novel landmark annotation scheme that facilitates the generation of landmark ground truth on larger clinical datasets.MethodsIn our annotation scheme, landmarks are equally distributed over all time points of all available dataset cases and annotated by multiple observers on a per-pair basis. The scheme is used to annotate 26 DCE-MRI of the liver. A subset of the ground truth is used to optimize parameters of a deformable motion correction. Several variants of the motion correction are evaluated on the remaining cases with respect to distances of corresponding landmarks after registration, deformation field properties, and qualitative measures.ResultsA landmark ground truth on 26 cases could be generated in under 12 h per observer with a mean inter-observer distance below the mean voxel diagonal. Furthermore, the landmarks are spatially well distributed within the liver. Parameter optimization significantly improves the performance of the motion correction, and landmark distance after registration is 2 mm. Qualitative evaluation of the motion correction reflects the quantitative results.ConclusionsThe annotation scheme makes a landmark-based evaluation of motion corrections for hepatic DCE-MRI practically feasible for larger clinical datasets. The comparably large number of cases enables both optimization and evaluation of motion correction methods.
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Project description:Stimulus images can be reconstructed from visual cortical activity. However, our perception of stimuli is shaped by both stimulus-induced and top-down processes, and it is unclear whether and how reconstructions reflect top-down aspects of perception. Here, we investigate the effect of attention on reconstructions using fMRI activity measured while subjects attend to one of two superimposed images. A state-of-the-art method is used for image reconstruction, in which brain activity is translated (decoded) to deep neural network (DNN) features of hierarchical layers then to an image. Reconstructions resemble the attended rather than unattended images. They can be modeled by superimposed images with biased contrasts, comparable to the appearance during attention. Attentional modulations are found in a broad range of hierarchical visual representations and mirror the brain-DNN correspondence. Our results demonstrate that top-down attention counters stimulus-induced responses, modulating neural representations to render reconstructions in accordance with subjective appearance.
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