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 We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all sub-regions simultaneously Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource

/pdf/the-multimodal-brain-tumor-image-segmentation-benchmark-2gfraj98dk.pdf

The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)

QUITE apart from the academic consideration that vital and medical statistics now form an obligatory part of the education of students seeking the University of London's diploma in public health, the demand for information about the methods of vital and medical statistics is increasing. The most casual reader of the newspapers is now aware that population problems are of serious practical importance and that the publications of the General Register Office cannot be ignored. It is scarcely an exaggeration to say that the recently issued preliminary report on the census of 1931 is one of the most sensational documents which has appeared for years, and that he who reads it intelligently will understand what is meant by saying that civilisation is in the melting pot. An Introduction to Medical Statistics. By Hilda M. Woods William T. Russell. Pp. x + 125. (London: P. S. King and Son, Ltd., 1931.) 7s. 6d.

/pdf/an-introduction-to-medical-statistics-58gm2cuxfv.pdf

An Introduction to Medical Statistics

Automatic whole-brain extraction from magnetic resonance images (MRI), also known as skull stripping, is a key component in most neuroimage pipelines. As the first element in the chain, its robustness is critical for the overall performance of the system. Many skull stripping methods have been proposed, but the problem is not considered to be completely solved yet. Many systems in the literature have good performance on certain datasets (mostly the datasets they were trained/tuned on), but fail to produce satisfactory results when the acquisition conditions or study populations are different. In this paper we introduce a robust, learning-based brain extraction system (ROBEX). The method combines a discriminative and a generative model to achieve the final result. The discriminative model is a Random Forest classifier trained to detect the brain boundary; the generative model is a point distribution model that ensures that the result is plausible. When a new image is presented to the system, the generative model is explored to find the contour with highest likelihood according to the discriminative model. Because the target shape is in general not perfectly represented by the generative model, the contour is refined using graph cuts to obtain the final segmentation. Both models were trained using 92 scans from a proprietary dataset but they achieve a high degree of robustness on a variety of other datasets. ROBEX was compared with six other popular, publicly available methods (BET, BSE, FreeSurfer, AFNI, BridgeBurner, and GCUT) on three publicly available datasets (IBSR, LPBA40, and OASIS, 137 scans in total) that include a wide range of acquisition hardware and a highly variable population (different age groups, healthy/diseased). The results show that ROBEX provides significantly improved performance measures for almost every method/dataset combination.

/pdf/robust-brain-extraction-across-datasets-and-comparison-with-2z6hms1c27.pdf

Robust Brain Extraction Across Datasets and Comparison With Publicly Available Methods

Integration of visual characterization of emphysema and airway abnormalities with physiologic and quantitative CT assessment permits categorization of chronic obstructive pulmonary disease into distinct structurally and functionally defined subtypes.

/pdf/ct-definable-subtypes-of-chronic-obstructive-pulmonary-42hf1lgqbk.pdf

CT-Definable Subtypes of Chronic Obstructive Pulmonary Disease: A Statement of the Fleischner Society.

International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future.

https://hal.archives-ouvertes.fr/hal-01958848/document

Why rankings of biomedical image analysis competitions should be interpreted with care

Chronic obstructive pulmonary disease (COPD) is characterized by variable contributions of emphysema and airway disease on computed tomography (CT), and still little is known on their temporal evolution. We hypothesized that quantitative CT (QCT) is able to detect short-time changes in a cohort of patients with very severe COPD. Two paired in- and expiratory CT each from 70 patients with avg. GOLD stage of 3.6 (mean age = 66 ± 7.5, mean FEV1/FVC = 35.28 ± 7.75) were taken 3 months apart and analyzed by fully automatic software computing emphysema (emphysema index (EI), mean lung density (MLD)), air-trapping (ratio expiration to inspiration of mean lung attenuation (E/I MLA), relative volume change between − 856 HU and − 950 HU (RVC856–950)), and parametric response mapping (PRM) parameters for each lobe separately and the whole lung. Airway metrics measured were wall thickness (WT) and lumen area (LA) for each airway generation and the whole lung. The average of the emphysema parameters (EI, MLD) increased significantly by 1.5% (p < 0.001) for the whole lung, whereas air-trapping parameters (E/I MLA, RVC856–950) were stable. PRMEmph increased from 34.3 to 35.7% (p < 0.001), whereas PRMNormal decrased from 23.6% to 22.8% (p = 0.012). WT decreased significantly from 1.17 ± 0.18 to 1.14 ± 0.19 mm (p = 0.036) and LA increased significantly from 25.08 ± 4.49 to 25.84 ± 4.87 mm2 (p = 0.041) for the whole lung. The generation-based analysis showed heterogeneous results. QCT detects short-time progression of emphysema in severe COPD. The changes were partly different among lung lobes and airway generations, indicating that QCT is useful to address the heterogeneity of COPD progression. • QCT detects short-time progression of emphysema in severe COPD in a 3-month period.
 • QCT is able to quantify even slight parenchymal changes, which were not detected by spirometry.
 • QCT is able to address the heterogeneity of COPD, revealing inconsistent changes individual lung lobes and airway generations.

Quantitative CT detects progression in COPD patients with severe emphysema in a 3-month interval.

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Quantitative CT detects progression in COPD patients with severe emphysema in a 3-month interval.