Search

Time-resolved volumetric magnetic resonance imaging (4D MRI) could be used to address organ motion in image-guidedinterventions like tumor ablation. Current 4D reconstruction techniques are unsuitable for most interventional settings becausethey are limited to specific breathing phases, lack temporal/spatial resolution, and have long prior acquisitions or reconstructiontimes. Deep learning-based (DL) 4D MRI approaches promise to overcome these shortcomings but are sensitive to anotherproblem, which is domain shift. This work shows that transfer learning (TL) can help alleviate this key challenge. Data from20 healthy subjects were acquired and split into 16 source and 4 target domain subjects. We compare models trained fromscratch on target domain data with models fine-tuned from a pre-trained model. Significant improvements (P

Background and Objective: Ultrasound (US) devices are often used in percutanous interventions. Due to their low image quality, the US image slices are aligned with pre-operative Computed Tomography/Magnetic Resonance Imaging (CT/MRI) images to enable better visibilities of anatomies during the intervention. This work aims at improving the deep learning one shot registration by using less loops through deep learning networks.Methods: We propose two cascade networks which aim at improving registration accuracy by less loops. The InitNet-Regression-LoopNet (IRL) network applies the plane regression method to detect the orientation of the predicted plane derived from the previous loop, then corrects input CT/MRI volume orientation and improves the prediction iteratively. The InitNet-LoopNet-MultiChannel (ILM) comprises two cascade networks, where an InitNet is trained with low resolution images toperform coarse registration. Then, a LoopNet wraps the high resolution images and result of the previous loop into a three channel input and trained to improve prediction accuracy in every loop. Results: We benchmark the two cascade networks on 1035 clinical images from 52 patients , yielding an improved registration accuracy with LoopNet. The IRL achieved an average angle error of 13.3° and an average distance error of 4.5 millimieter. It out-performs the ILM network with angle error 17.4° and distance error 4.9 millimeter and the InitNet with angle error 18.6° and distance error 4.9 millimeter. Our results show the efficiency of the proposed registration networks, which have the potential to improve the robustness and accuracy of intraoperative patient registration.

Preoperative assessment of the proximity of critical structures to the tumors is crucial in avoiding unnecessary damage during prostate cancer treatment. A patient-specific 3D anatomical model of those structures, namely the neurovascular bundles (NVB) and the external urethral sphincters (EUS), can enable physicians to perform such assessments intuitively. As a crucial step to generate a patient-specific anatomical model from preoperative MRI in a clinical routine, we propose a multi-class automatic segmentation based on an anisotropic convolutional network. Our specific challenge is to train the network model on a unique source dataset only available at a single clinical site and deploy it to another target site without sharing the original images or labels. As network models trained on data from a single source suffer from quality loss due to the domain shift, we propose a semi-supervised domain adaptation (DA) method to refine the model’s performance in the target domain. Our DA method combines transfer learning and uncertainty guided self-learning based on deep ensembles. Experiments on the segmentation of the prostate, NVB, and EUS, show significant performance gain with the combination of those techniques compared to pure TL and the combination of TL with simple self-learning ($${p} p < 0.005 for all structures using a Wilcoxon’s signed-rank test). Results on a different task and data (Pancreas CT segmentation) demonstrate our method’s generic application capabilities. Our method has the advantage that it does not require any further data from the source domain, unlike the majority of recent domain adaptation strategies. This makes our method suitable for clinical applications, where the sharing of patient data is restricted.

Recent studies demonstrated the eligibility of convolutional neural networks (CNNs) for solving the image registration problem. CNNs enable faster transformation estimation and greater generalization capability needed for better support during medical interventions. Conventional fully-supervised training requires a lot of high-quality ground truth data such as voxel-to-voxel transformations, which typically are attained in a too tedious and error-prone manner. In our work, we use weakly-supervised learning, which optimizes the model indirectly only via segmentation masks that are a more accessible ground truth than the deformation fields. Concerning the weak supervision, we investigate two segmentation similarity measures: multiscale Dice similarity coefficient (mDSC) and the similarity between segmentation-derived signed distance maps (SDMs). We show that the combination of mDSC and SDM similarity measures results in a more accurate and natural transformation pattern together with a stronger gradient coverage. Furthermore, we introduce an auxiliary input to the neural network for the prior information about the prostate location in the MR sequence, which mostly is available preoperatively. This approach significantly outperforms the standard two-input models. With weakly labelled MR-TRUS prostate data, we showed registration quality comparable to the state-of-the-art deep learning-based method.

In interstitial high-dose rate brachytherapy, liver cancer is treated by internal radiation, requiring percutaneous placement of applicators within or close to the tumor. To maximize utility, the optimal applicator configuration is pre-planned on magnetic resonance images. The pre-planned configuration is then implemented via a magnetic resonance-guided intervention. Mapping the pre-planning information onto interventional data would reduce the radiologist’s cognitive load during the intervention and could possibly minimize discrepancies between optimally pre-planned and actually placed applicators. We propose a fast and robust two-step registration framework suitable for interventional settings: first, we utilize a multi-resolution rigid registration to correct for differences in patient positioning (rotation and translation). Second, we employ a novel iterative approach alternating between bias field correction and Markov random field deformable registration in a multi-resolution framework to compensate for non-rigid movements of the liver, the tumors and the organs at risk. In contrast to existing pre-correction methods, our multi-resolution scheme can recover bias field artifacts of different extents at marginal computational costs. We compared our approach to deformable registration via B-splines, demons and the SyN method on 22 registration tasks from eleven patients. Results showed that our approach is more accurate than the contenders for liver as well as for tumor tissues. We yield average liver volume overlaps of 94.0 ± 2.7% and average surface-to-surface distances of 2.02 ± 0.87 mm and 3.55 ± 2.19 mm for liver and tumor tissue, respectively. The reported distances are close to (or even below) the slice spacing (2.5 – 3.0 mm) of our data. Our approach is also the fastest, taking 35.8 ± 12.8 s per task. The presented approach is sufficiently accurate to map information available from brachytherapy pre-planning onto interventional data. It is also reasonably fast, providing a starting point for computer-aidance during intervention.

The extraction of spines from medical records in a fast yet accurate way is a challenging task, especially for large data sets. Addressing this issue, we present a framework based on convolutional neural networks for the reconstruction of the spinal shape and curvature, making statistical assessments feasible on epidemiological scale. Our method uses a two-step strategy. First, anchor vertebrae and the spinal centerline in between them get extracted. Second, the centerlines are transformed into a common coordinate system to enable comparisons and statistical assessments across subjects. Our networks were trained on 103 subjects, where we achieved accuracies of 3.3 mm on average, taking at most 1 s per record, which eases the handling of even very large cohorts. Without any further training, we validated our model on study data of about 3400 subjects with only 10 cases of failure, which demonstrates the robustness of our method with respect to the natural variability in spinal shape and curvature. A thorough statistical analysis of the results underpins the importance of our work. Specifically, we show that the spinal curvature is significantly influenced by the body mass index of a subject. Moreover, we show that the same findings arise when Cobb angles are considered instead of direct curvature measures. To this end, we propose a generalization of classical Cobb angles that can be evaluated algorithmically and can also serve as a useful (visual) tool for physicians in everyday clinical practice.

Background and Objective: We propose an automatic approach for fast vertebral body segmentation in three-dimensional magnetic resonance images of the whole spine. Previous works are limited to the lower thoracolumbar section and often take minutes to compute, which is problematic in clinical routine, for study data sets with numerous subjects or when the cervical or upper thoracic spine is to be analyzed. Methods: We address these limitations by a novel graph cut formulation based on vertebra patches extracted along the spine. For each patch, our formulation incorporates appearance and shape information derived from a task-specific convolutional neural network as well as star-convexity constraints that ensure a topologically correct segmentation of each vertebra. When segmenting vertebrae individually, ambiguities will occur due to overlapping segmentations of adjacent vertebrae. We tackle this problem by novel non-overlap constraints between neighboring patches based on so-called encoding swaps. The latter allow us to obtain a globally optimal multi-label segmentation of all vertebrae in polynomial time. Results: We validated our approach on two data sets. The first contains T1- and T2-weighted whole spine images of 64 subjects with varying health conditions. The second comprises 23 T2-weighted thoracolumbar images of young healthy adults and is publicly available. Our method yielded Dice coefficients of 93.8 ± 2.6% and 96.0 ± 1.0% for both data sets with a run time of 1.35 ± 0.08 s and 0.90 ± 0.03 s per vertebra on consumer hardware. A complete whole spine segmentation took 32.4 ± 1.92 s on average. Conclusions: Our results are superior to those of previous works at a fraction of their run time, which illustrates the efficiency and effectiveness of our whole spine segmentation approach.

Individualized and accurate segmentations of the prostate are essential for diagnosis as well as therapy planning in prostate cancer (PCa). Most of the previously proposed prostate segmentation approaches rely purely on axial MRI scans, which suffer from low out-of-plane resolution. We propose a method that makes use of sagittal and coronal MRI scans to improve the accuracy of segmentation. These scans are typically acquired as standard of care for PCa staging, but are generally ignored by the segmentation algorithms. Our method is based on a multi-stream 3D convolutional neural network for the automatic extraction of isotropic high resolution segmentations from MR images. We evaluated segmentation performance on an isotropic high resolution ground truth (n = 40 subjects). The results show that the use of multi-planar volumes for prostate segmentation leads to improved segmentation results not only for the whole prostate (92.1% Dice similarity coefficient), but also in apex and base regions.

A rising number of epidemiological studies apply imaging technologies. Images are not features themselves but provide raw data from which features are extracted. Different to other applications of analysis of medical images the data is analyzed statistically across the cohort. It results in unique requirements regarding the development of methods to efficiently integrate varying domain knowledge into the process without compromising comparability of results across subjects or time. Examples from two different strategies are presented and discussed.