Boutiques: a flexible framework to integrate command-line applications in computing platforms

We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.

Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure

We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-theart algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning, …), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores.

Robustness of spatio-temporal regularization in perfusion MRI deconvolution: An application to acute ischemic stroke

PURPOSE

The robustness of a recently introduced globally convergent deconvolution algorithm with temporal and edge-preserving spatial regularization for the deconvolution of dynamic susceptibility contrast perfusion magnetic resonance imaging is assessed in the context of ischemic stroke.

THEORY AND METHODS

Ischemic tissues are not randomly distributed in the brain but form a spatially organized entity. The addition of a spatial regularization term allows to take into account this spatial organization contrarily to the sole temporal regularization approach which processes each voxel independently. The robustness of the spatial regularization in relation to shape variability, hemodynamic variability in tissues, noise in the magnetic resonance imaging apparatus, and uncertainty on the arterial input function selected for the deconvolution is addressed via an original in silico validation approach.

RESULTS

The deconvolution algorithm proved robust to the different sources of variability, outperforming temporal Tikhonov regularization in most realistic conditions considered. The limiting factor is the proper estimation of the arterial input function.

CONCLUSION

This study quantified the robustness of a spatio-temporal approach for dynamic susceptibility contrast-magnetic resonance imaging deconvolution via a new simulator. This simulator, now accessible online, is of wide applicability for the validation of any deconvolution algorithm. Magn Reson Med 78:1981-1990, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

OntoVIP: an ontology for the annotation of object models used for medical image simulation

This paper describes the creation of a comprehensive conceptualization of object models used in medical image simulation, suitable for major imaging modalities and simulators. The goal is to create an application ontology that can be used to annotate the models in a repository integrated in the Virtual Imaging Platform (VIP), to facilitate their sharing and reuse. Annotations make the anatomical, physiological and pathophysiological content of the object models explicit. In such an interdisciplinary context we chose to rely on a common integration framework provided by a foundational ontology, that facilitates the consistent integration of the various modules extracted from several existing ontologies, i.e. FMA, PATO, MPATH, RadLex and ChEBI. Emphasis is put on methodology for achieving this extraction and integration. The most salient aspects of the ontology are presented, especially the organization in model layers, as well as its use to browse and query the model repository.

A virtual imaging platform for multi-modality medical image simulation

This paper presents the Virtual Imaging Platform (VIP), a platform accessible at http://vip.creatis.insa-lyon.fr to facilitate the sharing of object models and medical image simulators, and to provide access to distributed computing and storage resources. A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit computing and storage resources. Simulation results obtained in four image modalities and with different models show that VIP is versatile and robust enough to support large simulations. The platform currently has 200 registered users who consumed 33 years of CPU time in 2011.

Modifications of spontaneous cerebral blood flow oscillations during cardiopulmonary bypass

Spontaneous slow waves are present in the systemic circulation including the intracranial compartment. They are supposed to reflect the cerebral autoregulation. We hypothesised that in the absence of cardio respiratory variability, during cardiopulmonary bypass (CPB), we should reveal extreme physiologic controls.

MATERIAL/METHODS

Ten patients were included. Arterial blood pressure (ABP, radial invasive), extracorporeal circuitry pressure and cerebral blood flow velocity (CBFV, middle cerebral artery) were recorded. We analysed the slow waves in the B (8 to 50) and the UB (>50 to 200) bands (in milli-Hz). The analysis, before and during CPB, was performed in the tine domain (correlation coefficient, entropy, mean quantity of mutual information, relative entropy) and in the frequency domain (spectrogram, frequency spectrum, coherence).

RESULTS

CPB dramatically changed monitored signals decreasing their entropy and revealing a dominant CBFV 70 mHz-frequency and a dominant ABP 9 mHz-frequency. There was no association between the signals (p < 0.05). Before CPB we found complex patterns where B and UB waves were present.

CONCLUSION

We hypothesised that CPB provoked a highly protective mechanism, reducing the fluctuations of CBF, by a deactivation of B waves, revealing monotonous UB waves.

Slow pressure waves in the cranial enclosure

Slowly varying pressure oscillations in the cranial enclosure are well known, especially intracranial pressure waves as best described by the pioneering works of Janny and Lundberg. Nevertheless, in spite of over twenty five years research on intracranial pressure waves, their origin and regulation remain unclear but are often considered only as pathological. Our aim was to review data on these phenomena to clarify their biological status and the role that they could play in the management of patients suffering from such intracranial neurosurgical diseases as intracranial hypertension, severe head injury, and hydrocephalus. It appears that these pressure waves reveal important information on the function of the cerebral vasculature and as such have significance for influencing intracranial compliance. Pressure waves are also closely associated with autoregulation, in particular dynamic autoregulation. It seems evident that they are not only pathophysiological but also physiological, linked with other biological parameters such as the neurovegetative cardiovascular system, breathing, and sleeping. This study shows that it is not only important to continue to explore these slow waves, but also the methods of analysis in order to more fully clarify their clinical significance.