MASCG: Multi-Atlas Segmentation Constrained Graph method for accurate segmentation of hip CT images

This paper addresses the issue of fully automatic segmentation of a hip CT image with the goal to preserve the joint structure for clinical applications in hip disease diagnosis and treatment. For this purpose, we propose a Multi-Atlas Segmentation Constrained Graph (MASCG) method. The MASCG method uses multi-atlas based mesh fusion results to initialize a bone sheetness based multi-label graph cut for an accurate hip CT segmentation which has the inherent advantage of automatic separation of the pelvic region from the bilateral proximal femoral regions. We then introduce a graph cut constrained graph search algorithm to further improve the segmentation accuracy around the bilateral hip joint regions. Taking manual segmentation as the ground truth, we evaluated the present approach on 30 hip CT images (60 hips) with a 15-fold cross validation. When the present approach was compared to manual segmentation, an average surface distance error of 0.30 mm, 0.29 mm, and 0.30 mm was found for the pelvis, the left proximal femur, and the right proximal femur, respectively. A further look at the bilateral hip joint regions demonstrated an average surface distance error of 0.16 mm, 0.21 mm and 0.20 mm for the acetabulum, the left femoral head, and the right femoral head, respectively.

PSHARE: Stata module to compute and graph percentile shares

-pshare- computes and graphs percentile shares from individual level data. Percentile shares are often used in inequality research to study the distribution of income or wealth. They are defined as differences between Lorenz ordinates of the outcome variable. Technically, the observations are sorted in increasing order of the outcome variable and the specified percentiles are computed from the running sum of the outcomes. Percentile shares are then computed as differences between percentiles, divided by total outcome. pshare requires moremata to be installed on the system; see ssc describe moremata.

Building the View Graph of a Category by Exploiting Image Realism

We propose a weakly supervised method to arrange images of a given category based on the relative pose between the camera and the object in the scene. Relative poses are points on a sphere centered at the object in a given canonical pose, which we call object viewpoints. Our method builds a graph on this sphere by assigning images with similar viewpoint to the same node and by connecting nodes if they are related by a small rotation. The key idea is to exploit a large unlabeled dataset to validate the likelihood of dominant 3D planes of the object geometry. A number of 3D plane hypotheses are evaluated by applying small 3D rotations to each hypothesis and by measuring how well the deformed images match other images in the dataset. Correct hypotheses will result in deformed images that correspond to plausible views of the object, and thus will likely match well other images in the same category. The identified 3D planes are then used to compute affinities between images related by a change of viewpoint. We then use the affinities to build a view graph via a greedy method and the maximum spanning tree.

LOGITCPRPLOT: Stata module to graph component-plus-residual plot for logistic regression

logitcprplot can be used after logistic regression for graphing a component-plus-residual plot (a.k.a. partial residual plot) for a given predictor, including a lowess, local polynomial, restricted cubic spline, fractional polynomial, penalized spline, regression spline, running line, or adaptive variable span running line smooth

CPRPLOT2: Stata module to graph component-plus-residual plots for transformed regressors

cprplot2 is a variation of official Stata's cprplot and is used for graphing component-plus-residual plots (a.k.a. partial residual plots). Additional features (compared to cprplot): (1) cprplot2 can handle variables that enter the model repeatedly via different transformations (for example, polynomials). (2) cprplot2 can display component-plus-residual plots using the original units for transformed variables in the model. (3) A wrapper is provided to quickly display several component-plus-residual plots in a single image.

Benchmarking numerical models of brittle thrust wedges

We report quantitative results from three brittle thrust wedge experiments, comparing numerical results directly with each other and with corresponding analogue results. We first test whether the participating codes reproduce predictions from analytical critical taper theory. Eleven codes pass the stable wedge test, showing negligible internal deformation and maintaining the initial surface slope upon horizontal translation over a frictional interface. Eight codes participated in the unstable wedge test that examines the evolution of a wedge by thrust formation from a subcritical state to the critical taper geometry. The critical taper is recovered, but the models show two deformation modes characterised by either mainly forward dipping thrusts or a series of thrust pop-ups. We speculate that the two modes are caused by differences in effective basal boundary friction related to different algorithms for modelling boundary friction. The third experiment examines stacking of forward thrusts that are translated upward along a backward thrust. The results of the seven codes that run this experiment show variability in deformation style, number of thrusts, thrust dip angles and surface slope. Overall, our experiments show that numerical models run with different numerical techniques can successfully simulate laboratory brittle thrust wedge models at the cm-scale. In more detail, however, we find that it is challenging to reproduce sandbox-type setups numerically, because of frictional boundary conditions and velocity discontinuities. We recommend that future numerical-analogue comparisons use simple boundary conditions and that the numerical Earth Science community defines a plasticity test to resolve the variability in model shear zones.

Benchmarking analogue models of brittle thrust wedges

We performed a quantitative comparison of brittle thrust wedge experiments to evaluate the variability among analogue models and to appraise the reproducibility and limits of model interpretation. Fifteen analogue modeling laboratories participated in this benchmark initiative. Each laboratory received a shipment of the same type of quartz and corundum sand and all laboratories adhered to a stringent model building protocol and used the same type of foil to cover base and sidewalls of the sandbox. Sieve structure, sifting height, filling rate, and details on off-scraping of excess sand followed prescribed procedures. Our analogue benchmark shows that even for simple plane-strain experiments with prescribed stringent model construction techniques, quantitative model results show variability, most notably for surface slope, thrust spacing and number of forward and backthrusts. One of the sources of the variability in model results is related to slight variations in how sand is deposited in the sandbox. Small changes in sifting height, sifting rate, and scraping will result in slightly heterogeneous material bulk densities, which will affect the mechanical properties of the sand, and will result in lateral and vertical differences in peak and boundary friction angles, as well as cohesion values once the model is constructed. Initial variations in basal friction are inferred to play the most important role in causing model variability. Our comparison shows that the human factor plays a decisive role, and even when one modeler repeats the same experiment, quantitative model results still show variability. Our observations highlight the limits of up-scaling quantitative analogue model results to nature or for making comparisons with numerical models. The frictional behavior of sand is highly sensitive to small variations in material state or experimental set-up, and hence, it will remain difficult to scale quantitative results such as number of thrusts, thrust spacing, and pop-up width from model to nature.