Advanced Medical Image Registration Methods for Quantitative Imaging and Multi-Channel Images

This thesis proposes advanced medical image registration methods for applications that can be grouped in two broad themes. The first theme focuses on registration techniques increasing the reliability of _quantitative measurements_ extracted from sets of medical images. The second theme that is considered in this thesis is the registration of _multi-channel_ images

The accuracy of ADC measurements in liver is improved by a tailored and computationally efficient local-rigid registration algorithm

This study describes post-processing methodologies to reduce the effects of physiological motion in measurements of apparent diffusion coefficient (ADC) in the liver. The aims of the study are to improve the accuracy of ADC measurements in liver disease to support quantitative clinical characterisation and reduce the number of patients required for sequential studies of disease progression and therapeutic effects. Two motion correction methods are compared, one based on non-rigid registration (NRA) using freely available open source algorithms and the other a local-rigid registration (LRA) specifically designed for use with diffusion weighted magnetic resonance (DW-MR) data. Performance of these methods is evaluated using metrics computed from regional ADC histograms on abdominal image slices from healthy volunteers. While the non-rigid registration method has the advantages of being applicable on the whole volume and in a fully automatic fashion, the local-rigid registration method is faster while maintaining the integrity of the biological structures essential for analysis of tissue heterogeneity. Our findings also indicate that the averaging commonly applied to DW-MR images as part of the acquisition protocol should be avoided if possible

Registration of magnetic resonance and computed tomography images in patients with oral squamous cell carcinoma for three-dimensional vir

The aim of this study was to evaluate and present an automated method for registration of magnetic resonance imaging (MRI) and computed tomography (CT) or cone beam CT (CBCT) images of the mandibular region for patients with oral squamous cell carcinoma (OSCC). Registered MRI and (CB)CT could facilitate the three-dimensional virtual planning of surgical guides employed for resection and reconstruction in patients with OSCC with mandibular invasion. MRI and (CB)CT images were collected retrospectively from 19 patients. MRI images were aligned with (CB)CT images employing a rigid registration approach (stage 1), a rigid registration approach using a mandibular mask (stage 2), and two non-rigid registration approaches (stage 3). Registration accuracy was quantified by the mean target registration error (mTRE), calculated over a set of landmarks annotated by two observers. Stage 2 achieved the best registration result, with an mTRE of 2.5 ± 0.7 mm, which was comparable to the inter- and intra-observer variabilities of landmark placement in MRI. Stage 2 was significantly better aligned compared to all approaches in stage 3. In conclusion, this study demonstrated that rigid registration with the use of a mask is an appropriate image registration method for aligning MRI and (CB)CT images of the mandibular region in patients with OSCC

Multidisciplinary investigation on cold seeps with vigorous gas emissions in the Sea of Marmara (MarsiteCruise): Strategy for site detection and sampling and first scientific outcome

MarsiteCruise was undertaken in October/November 2014 in the Sea of Marmara to gain detailed insight into the fate of fluids migrating within the sedimentary column and partially released into the water column. The overall objective of the project was to achieve a more global understanding of cold-seep dynamics in the context of a major active strike-slip fault. Five remotely operated vehicle (ROV) dives were performed at selected areas along the North Anatolian Fault and inherited faults. To efficiently detect, select and sample the gas seeps, we applied an original procedure. It combines sequentially (1) the acquisition of ship-borne multibeam acoustic data from the water column prior to each dive to detect gas emission sites and to design the tracks of the ROV dives, (2) in situ and real-time Raman spectroscopy analysis of the gas stream, and (3) onboard determination of molecular and isotopic compositions of the collected gas bubbles. The in situ Raman spectroscopy was used as a decision-making tool to evaluate the need for continuing with the sampling of gases from the discovered seep, or to move to another one. Push cores were gathered to study buried carbonates and pore waters at the surficial sediment, while CTD-Rosette allowed collecting samples to measure dissolved-methane concentration within the water column followed by a comparison with measurements from samples collected with the submersible Nautile during the Marnaut cruise in 2007. Overall, the visited sites were characterized by a wide diversity of seeps. CO2- and oil-rich seeps were found at the westernmost part of the sea in the Tekirdag Basin, while amphipods, anemones and coral populated the sites visited at the easternmost part in the Cinarcik Basin. Methane-derived authigenic carbonates and bacterial mats were widespread on the seafloor at all sites with variable size and distributions. The measured methane concentrations in the water column were up to 377 μmol, and the dissolved pore-water profiles indicated the occurrence of sulfate depleting processes accompanied with carbonate precipitation. The pore-water profiles display evidence of biogeochemical transformations leading to the fast depletion of seawater sulfate within the first 25-cm depth of the sediment. These results show that the North Anatolian Fault and inherited faults are important migration paths for fluids for which a significant part is discharged into the water column, contributing to the increase of methane concentration at the bottom seawater and favoring the development of specific ecosystems

Société du savoir

International audienc

Société du savoir

Éditeur Le PommierInternational audienc

Comparison of Local-rigid and Non-rigid Registration of Diffusion Weighted MRI for Improved Estimation of ADC. Comparison of Local-rigid and Non-rigid Registration of Diffusion Weighted MRI for Improved Estimation of ADC

Abstract Our aim is to develop methodologies for the determination of ADC, suitable for use in patient management and drug trials. In this paper we demonstrate improvements in ADC measurement which at the same time maintain the biological structures essential for analysis of tissue heterogeneity. Two motion correction methods are compared, one based upon non-rigid registration using freely available open source algorithms and the other a purpose designed local rigid registration. Performance of these methods is evaluated using metrics computed from regional ADC histograms. While the nonrigid registration method has the advantages of being applicable on the whole volume and in a fully automatic fashion, the local rigid registration method is much faster and also provides advantages with regard to data smoothness by avoiding interpolation and sub-sampling. Our study also shows that the averaging commonly applied to DW-MR images as part of the acquisition protocol should be avoided if at all possible

New software library of geometrical primitives for modeling of solids used in Monte Carlo detector simulations

We present our effort for the creation of a new software library of geometrical primitives, which are used for solid modeling in Monte Carlo detector simulations. We plan to replace and unify the current implementations for geometrical primitive classes in the software projects Geant4 and ROOT with this library. Each solid is implemented as a C++ class providing methods to compute distances of rays to the surface of a solid or to find whether a position is located inside, outside or on the surface of the solid. A numerical tolerance is used for determining whether a position is on the surface. The class methods also contain basic support for visualization. We use dedicated test suites for the validation of the code, these also include performance and consistency tests used for the analysis of candidate implementations of class methods for the new library. We have implemented simple adapter classes to allow the use of the new optimized solids with Geant4 and ROOT geometries

A simple method for detection of major phenotypic abnormalities in myelodysplastic syndromes: expression of CD56 in CMML.

International audienceUsing a very simple flow cytometry protocol, we found that CD36 and CD117 on granulocytes and CD56 on monocytes were the major bone marrow phenotypic aberrations in patients with myelodysplasia, including CMML. CD56 on monocytes was associated with CMML. Importantly, phenotypic aberrations were lost on blood cells, except for CD56

Influence of image registration on apparent diffusion coefficient images computed from free-breathing diffusion MR images of the abdomen

BackgroundTo evaluate the influence of image registration on apparent diffusion coefficient (ADC) images obtained from abdominal free-breathing diffusion-weighted MR images (DW-MRIs). MethodsA comprehensive pipeline based on automatic three-dimensional nonrigid image registrations is developed to compensate for misalignments in DW-MRI datasets obtained from five healthy subjects scanned twice. Motion is corrected both within each image and between images in a time series. ADC distributions are compared with and without registration in two abdominal volumes of interest (VOIs). The effects of interpolations and Gaussian blurring as alternative strategies to reduce motion artifacts are also investigated. ResultsAmong the four considered scenarios (no processing, interpolation, blurring and registration), registration yields the best alignment scores. Median ADCs vary according to the chosen scenario: for the considered datasets, ADCs obtained without processing are 30% higher than with registration. Registration improves voxelwise reproducibility at least by a factor of 2 and decreases uncertainty (Frechet-Cramer-Rao lower bound). Registration provides similar improvements in reproducibility and uncertainty as acquiring four times more data. ConclusionPatient motion during image acquisition leads to misaligned DW-MRIs and inaccurate ADCs, which can be addressed using automatic registration. J. Magn. Reson. Imaging 2015;42:315-330