PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI

In this paper we present a novel method for the correction of motion artifacts that are present in fetal Magnetic Resonance Imaging (MRI) scans of the whole uterus. Contrary to current slice-to-volume registration (SVR) methods, requiring an inflexible anatomical enclosure of a single investigated organ, the proposed patch-to-volume reconstruction (PVR) approach is able to reconstruct a large field of view of non-rigidly deforming structures. It relaxes rigid motion assumptions by introducing a specific amount of redundant information that is exploited with parallelized patch-wise optimization, super-resolution, and automatic outlier rejection. We further describe and provide an efficient parallel implementation of PVR allowing its execution within reasonable time on commercially available graphics processing units (GPU), enabling its use in the clinical practice. We evaluate PVR's computational overhead compared to standard methods and observe improved reconstruction accuracy in presence of affine motion artifacts of approximately 30% compared to conventional SVR in synthetic experiments. Furthermore, we have evaluated our method qualitatively and quantitatively on real fetal MRI data subject to maternal breathing and sudden fetal movements. We evaluate peak-signal-to-noise ratio (PSNR), structural similarity index (SSIM), and cross correlation (CC) with respect to the originally acquired data and provide a method for visual inspection of reconstruction uncertainty. With these experiments we demonstrate successful application of PVR motion compensation to the whole uterus, the human fetus, and the human placenta.Comment: 10 pages, 13 figures, submitted to IEEE Transactions on Medical Imaging. v2: wadded funders acknowledgements to preprin

Automated detection of brain abnormalities in neonatal hypoxia ischemic injury from MR images.

We compared the efficacy of three automated brain injury detection methods, namely symmetry-integrated region growing (SIRG), hierarchical region splitting (HRS) and modified watershed segmentation (MWS) in human and animal magnetic resonance imaging (MRI) datasets for the detection of hypoxic ischemic injuries (HIIs). Diffusion weighted imaging (DWI, 1.5T) data from neonatal arterial ischemic stroke (AIS) patients, as well as T2-weighted imaging (T2WI, 11.7T, 4.7T) at seven different time-points (1, 4, 7, 10, 17, 24 and 31 days post HII) in rat-pup model of hypoxic ischemic injury were used to assess the temporal efficacy of our computational approaches. Sensitivity, specificity, and similarity were used as performance metrics based on manual ('gold standard') injury detection to quantify comparisons. When compared to the manual gold standard, automated injury location results from SIRG performed the best in 62% of the data, while 29% for HRS and 9% for MWS. Injury severity detection revealed that SIRG performed the best in 67% cases while 33% for HRS. Prior information is required by HRS and MWS, but not by SIRG. However, SIRG is sensitive to parameter-tuning, while HRS and MWS are not. Among these methods, SIRG performs the best in detecting lesion volumes; HRS is the most robust, while MWS lags behind in both respects

Semantically Guided Depth Upsampling

We present a novel method for accurate and efficient up- sampling of sparse depth data, guided by high-resolution imagery. Our approach goes beyond the use of intensity cues only and additionally exploits object boundary cues through structured edge detection and semantic scene labeling for guidance. Both cues are combined within a geodesic distance measure that allows for boundary-preserving depth in- terpolation while utilizing local context. We model the observed scene structure by locally planar elements and formulate the upsampling task as a global energy minimization problem. Our method determines glob- ally consistent solutions and preserves fine details and sharp depth bound- aries. In our experiments on several public datasets at different levels of application, we demonstrate superior performance of our approach over the state-of-the-art, even for very sparse measurements.Comment: German Conference on Pattern Recognition 2016 (Oral

Superpixel-based Two-view Deterministic Fitting for Multiple-structure Data

This paper proposes a two-view deterministic geometric model fitting method, termed Superpixel-based Deterministic Fitting (SDF), for multiple-structure data. SDF starts from superpixel segmentation, which effectively captures prior information of feature appearances. The feature appearances are beneficial to reduce the computational complexity for deterministic fitting methods. SDF also includes two original elements, i.e., a deterministic sampling algorithm and a novel model selection algorithm. The two algorithms are tightly coupled to boost the performance of SDF in both speed and accuracy. Specifically, the proposed sampling algorithm leverages the grouping cues of superpixels to generate reliable and consistent hypotheses. The proposed model selection algorithm further makes use of desirable properties of the generated hypotheses, to improve the conventional fit-and-remove framework for more efficient and effective performance. The key characteristic of SDF is that it can efficiently and deterministically estimate the parameters of model instances in multi-structure data. Experimental results demonstrate that the proposed SDF shows superiority over several state-of-the-art fitting methods for real images with single-structure and multiple-structure data.Comment: Accepted by European Conference on Computer Vision (ECCV