The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS).

In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences. Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low- and high-grade glioma patients-manually annotated by up to four raters-and to 65 comparable scans generated using tumor image simulation software. Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74%-85%), illustrating the difficulty of this task.

Laplacian forests: semantic image segmentation by guided bagging.

This paper presents a new, efficient and accurate technique for the semantic segmentation of medical images. The paper builds upon the successful random decision forests model and improves on it by modifying the way in which randomness is injected into the tree training process. The contribution of this paper is two-fold.

Quantifying progression of multiple sclerosis via classification of depth videos.

This paper presents new learning-based techniques for measuring disease progression in Multiple Sclerosis (MS) patients. Our system aims to augment conventional neurological examinations by adding quantitative evidence of disease progression. An off-the-shelf depth camera is used to image the patient at the examination, during which he/she is asked to perform carefully selected movements.

Robust registration of longitudinal spine CT.

Accurate and reliable registration of longitudinal spine images is essential for assessment of disease progression and surgical outcome. Implementing a fully automatic and robust registration for clinical use, however, is challenging since standard registration techniques often fail due to poor initial alignment. The main causes of registration failure are the small overlap between scans which focus on different parts of the spine and/or substantial change in shape (e.

Image quality transfer via random forest regression: applications in diffusion MRI.

This paper introduces image quality transfer. The aim is to learn the fine structural detail of medical images from high quality data sets acquired with long acquisition times or from bespoke devices and transfer that information to enhance lower quality data sets from standard acquisitions. We propose a framework for solving this problem using random forest regression to relate patches in the low-quality data set to voxel values in the high quality data set.

Vertebrae localization in pathological spine CT via dense classification from sparse annotations.

Accurate localization and identification of vertebrae in spinal imaging is crucial for the clinical tasks of diagnosis, surgical planning, and post-operative assessment. The main difficulties for automatic methods arise from the frequent presence of abnormal spine curvature, small field of view, and image artifacts caused by surgical implants. Many previous methods rely on parametric models of appearance and shape whose performance can substantially degrade for pathological cases.

Atlas encoding by randomized forests for efficient label propagation.

We propose a method for multi-atlas label propagation based on encoding the individual atlases by randomized classification forests. Most current approaches perform a non-linear registration between all atlases and the target image, followed by a sophisticated fusion scheme. While these approaches can achieve high accuracy, in general they do so at high computational cost.

Is synthesizing MRI contrast useful for inter-modality analysis?

Availability of multi-modal magnetic resonance imaging (MRI) databases opens up the opportunity to synthesize different MRI contrasts without actually acquiring the images. In theory such synthetic images have the potential to reduce the amount of acquisitions to perform certain analyses. However, to what extent they can substitute real acquisitions in the respective analyses is an open question.

Modality propagation: coherent synthesis of subject-specific scans with data-driven regularization.

We propose a general database-driven framework for coherent synthesis of subject-specific scans of desired modality, which adopts and generalizes the patch-based label propagation (LP) strategy. While modality synthesis has received increased attention lately, current methods are mainly tailored to specific applications. On the other hand, the LP framework has been extremely successful for certain segmentation tasks, however, so far it has not been used for estimation of entities other than categorical segmentation labels.

Neighbourhood approximation using randomized forests.

Leveraging available annotated data is an essential component of many modern methods for medical image analysis. In particular, approaches making use of the "neighbourhood" structure between images for this purpose have shown significant potential. Such techniques achieve high accuracy in analysing an image by propagating information from its immediate "neighbours" within an annotated database.

Decision forests for tissue-specific segmentation of high-grade gliomas in multi-channel MR.

We present a method for automatic segmentation of high-grade gliomas and their subregions from multi-channel MR images. Besides segmenting the gross tumor, we also differentiate between active cells, necrotic core, and edema. Our discriminative approach is based on decision forests using context-aware spatial features, and integrates a generative model of tissue appearance, by using the probabilities obtained by tissue-specific Gaussian mixture models as additional input for the forest.

Neighbourhood approximation forests.

Methods that leverage neighbourhood structures in high-dimensional image spaces have recently attracted attention. These approaches extract information from a new image using its "neighbours" in the image space equipped with an application-specific distance. Finding the neighbourhood of a given image is challenging due to large dataset sizes and costly distance evaluations.

Generalization of deformable registration in Riemannian Sobolev spaces.

In this work we discuss the generalized treatment of the deformable registration problem in Sobolev spaces. We extend previous approaches in two points: 1) by employing a general energy model which includes a regularization term, and 2) by changing the notion of distance in the Sobolev space by problem-dependent Riemannian metrics. The actual choice of the metric is such that it has a preconditioning effect on the problem, it is applicable to arbitrary similarity measures, and features a simple implementation.

Linear intensity-based image registration by Markov random fields and discrete optimization.

We propose a framework for intensity-based registration of images by linear transformations, based on a discrete Markov random field (MRF) formulation. Here, the challenge arises from the fact that optimizing the energy associated with this problem requires a high-order MRF model. Currently, methods for optimizing such high-order models are less general, easy to use, and efficient, than methods for the popular second-order models.

Deformable 2D-3D registration of vascular structures in a one view scenario.

Alignment of angiographic 3D scans to 2D projections is an important issue for 3D depth perception and navigation during interventions. Currently, in a setting where only one 2D projection is available, methods employing a rigid transformation model present the state of the art for this problem. In this work, we introduce a method capable of deformably registering 3D vessel structures to a respective single projection of the scene.

A novel intensity similarity metric with soft spatial constraint for a deformable image registration problem in radiation therapy.

In this paper we propose a novel similarity metric and a method for deformable registration of two images for a specific clinical application. The basic assumption in almost all deformable registration approaches is that there exist explicit correspondences between pixels across the two images. This principle is used to design image (dis)similarity metrics, such as sum of squared differences (SSD) or mutual information (MI).

A new and general method for blind shift-variant deconvolution of biomedical images.

We present a new method for blind deconvolution of multiple noisy images blurred by a shift-variant point-spread-function (PSF). We focus on a setting in which several images of the same object are available, and a transformation between these images is known. This setting occurs frequently in biomedical imaging, for example in microscopy or in medical ultrasound imaging.

Fast deformable registration of 3D-ultrasound data using a variational approach.

We present an intensity based deformable registration algorithm for 3D ultrasound data. The proposed method uses a variational approach and combines the characteristics of a multilevel algorithm and the properties of ultrasound data in order to provide a fast and accurate deformable registration method. In contrast to previously proposed approaches, we use no feature points and no interpolation technique, but compute a dense displacement field directly.

Dual cardiac-respiratory gated PET: implementation and results from a feasibility study.

Purpose: Spatial resolution in myocardial imaging is impaired by both cardiac and respiratory motion owing to motional blurring. We investigated the feasibility of a dual cardiac-respiratory gated positron emission tomography (PET) acquisition using a clinical PET/computer tomography (CT) scanner. We describe its implementation and present results on the respiratory motion observed.