Automatic segmentation of high-and low-field knee MRIs using knee image quantification with data from the osteoarthritis initiative

Clinical studies including thousands of magnetic resonance imaging (MRI) scans offer potential for pathogenesis research in osteoarthritis. However, comprehensive quantification of all bone, cartilage, and meniscus compartments is challenging. We propose a segmentation framework for fully automatic segmentation of knee MRI. The framework combines multiatlas rigid registration with voxel classification and was trained on manual segmentations with varying configurations of bones, cartilages, and menisci. The validation included high- and low-field knee MRI cohorts from the Center for Clinical and Basic Research, the osteoarthritis initiative (QAI), and the segmentation of knee images10 (SKI10) challenge. In total, 1907 knee MRIs were segmented during the evaluation. No segmentations were excluded. Our resulting OAI cartilage volume scores are available upon request. The precision and accuracy performances matched manual reader re-segmentation well. The cartilage volume scan-rescan precision was 4.9% (RMS CV). The Dice volume overlaps in the medial/lateral tibial/femoral cartilage compartments were 0.80 to 0.87. The correlations with volumes from independent methods were between 0.90 and 0.96 on the OAI scans. Thus, the framework demonstrated precision and accuracy comparable to manual segmentations. Finally, our method placed second for cartilage segmentation in the SKI10 challenge. The comprehensive validation suggested that automatic segmentation is appropriate for cohorts with thousands of scans

Mammographic texture resemblance generalizes as an independent risk factor for breast cancer

INTRODUCTION: Breast density has been established as a major risk factor for breast cancer. We have previously demonstrated that mammographic texture resemblance (MTR), recognizing the local texture patterns of the mammogram, is also a risk factor for breast cancer, independent of percent breast density. We examine if these findings generalize to another population. METHODS: Texture patterns were recorded in digitalized pre-diagnosis (3.7 years) film mammograms of a nested case–control study within the Dutch screening program (S1) comprising of 245 breast cancers and 250 matched controls. The patterns were recognized in the same study using cross-validation to form resemblance scores associated with breast cancer. Texture patterns from S1 were examined in an independent nested case–control study within the Mayo Mammography Health Study cohort (S2) of 226 cases and 442 matched controls: mammograms on average 8.5 years prior to diagnosis, risk factor information and percent mammographic density (PD) estimated using Cumulus were available. MTR scores estimated from S1, S2 and S1 + S2 (the latter two as cross-validations) were evaluated in S2. MTR scores were analyzed as both quartiles and continuously for association with breast cancer using odds ratios (OR) and adjusting for known risk factors including age, body mass index (BMI), and hormone usage. RESULTS: The mean ages of S1 and S2 were 58.0 ± 5.7 years and 55.2 ± 10.5 years, respectively. The MTR scores on S1 showed significant capability to discriminate cancers from controls (area under the operator characteristics curve (AUC) = 0.63 ± 0.02, P <0.001), which persisted after adjustment for PD. S2 showed an AUC of 0.63, 0.61, and 0.60 based on PD, MTR scores trained on S2, and MTR scores trained on S1, respectively. When adjusted for PD, MTR scores of S2 trained on S1 showed an association with breast cancer for the highest quartile alone: OR in quartiles of controls as reference; 1.04 (0.59 to 1.81); 0.95 (0.52 to 1.74); 1.84 (1.10 to 3.07) respectively. The combined continuous model with both PD and MTR scores based on S1 had an AUC of 0.66 ± 0.03. CONCLUSIONS: The local texture patterns associated with breast cancer risk in S1 were also an independent risk factor in S2. Additional textures identified in S2 did not significantly improve risk segregation. Hence, the textural patterns that indicated elevated risk persisted under differences in X-ray technology, population demographics, follow-up time and geography

Mammographic density and structural features can individually and jointly contribute to breast cancer risk assessment in mammography screening:a case-control study

BACKGROUND: Mammographic density is a well-established risk factor for breast cancer. We investigated the association between three different methods of measuring density or parenchymal pattern/texture on digitized film-based mammograms, and examined to what extent textural features independently and jointly with density can improve the ability to identify screening women at increased risk of breast cancer. METHODS: The study included 121 cases and 259 age- and time matched controls based on a cohort of 14,736 women with negative screening mammograms from a population-based screening programme in Denmark in 2007 (followed until 31 December 2010). Mammograms were assessed using the Breast Imaging-Reporting and Data System (BI-RADS) density classification, Tabár’s classification on parenchymal patterns and a fully automated texture quantification technique. The individual and combined association with breast cancer was estimated using binary logistic regression to calculate Odds Ratios (ORs) and the area under the receiver operating characteristic (ROC) curves (AUCs). RESULTS: Cases showed significantly higher BI-RADS and texture scores on average than controls (p < 0.001). All three methods were individually able to segregate women into different risk groups showing significant ORs for BI-RADS D3 and D4 (OR: 2.37; 1.32–4.25 and 3.93; 1.88–8.20), Tabár’s PIII and PIV (OR: 3.23; 1.20–8.75 and 4.40; 2.31–8.38), and the highest quartile of the texture score (3.04; 1.63–5.67). AUCs for BI-RADS, Tabár and the texture scores (continuous) were 0.63 (0.57–0–69), 0.65 (0.59–0–71) and 0.63 (0.57–0–69), respectively. Combining two or more methods increased model fit in all combinations, demonstrating the highest AUC of 0.69 (0.63-0.74) when all three methods were combined (a significant increase from standard BI-RADS alone). CONCLUSION: Our findings suggest that the (relative) amount of fibroglandular tissue (density) and mammographic structural features (texture/parenchymal pattern) jointly can improve risk segregation of screening women, using information already available from normal screening routine, in respect to future personalized screening strategies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12885-016-2450-7) contains supplementary material, which is available to authorized users

On Spatial Metamerism in Computational Vision

College London in collaboration with and hosted by Lecturer Lewis Griffin

Quaternions, interpolation and animation

The main topics of this technical report are quaternions, their mathematical properties, and how they can be used to rotate objects. We introduce quaternion mathematics and discuss why quaternions are a better choice for implementing rotation than the well-known matrix implementations. We then treat different methods for interpolation between series of rotations. During this treatment we give complete proofs for the correctness of the important interpolation methods Slerp and Squad. Inspired by our treatment of the different interpolation methods we develop our own interpolation method called Spring based on a set of objective constraints for an optimal interpolation curve. This results in a set of differential equations, whose analytical solution meets these constraints. Unfortunately, the set of differential equations cannot be solved analytically. As an alternative we propose a numerical solution for the differential equations. The different interpolation methods are visualized and commented. Finally we provide a thorough comparison of the two most convincing methods (Spring and Squad). Thereby, this report provides a comprehensiv

Mode estimation using pessimistic scale space tracking

Abstract. Estimation of the mode of a distribution over � from discrete samples is introduced and three methods for its solution are developed and evaluated. The first solution is based on Fréchet’s definition of central tendencies. We show that algorithms based on this approach have only limited success due to the non-differentiability of the Fréchet measures. The second solution is based on tracking maxima through a Scale Space built from the samples. We show that this is more accurate than the Fréchet approach, but that tracking to very fine scales is unwarranted and undesirable. For our third method we analyze the reliability of the information across scale using an exact bootstrap analysis. This leads to a modified version of the Scale Space approach where unreliable information is downgraded (pessimistically) so that tracking into such regions does not occur. This modification improves the accuracy of mode estimation. We conclude with demonstrations on high-dimensional real and synthetic data, which confirm the technique’s accuracy and utility.