| 31. |
- Borga, Magnus, 1965-, et al.
(författare)
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MRI-Based Body Composition Analysis
- 2022. - 1
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Ingår i: Basic Protocols in Foods and Nutrition. - New York, NY, United States : Springer Nature. - 9781071623442 ; , s. 307-334
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Bokkapitel (refereegranskat)abstract
- Magnetic resonance imaging (MRI) is considered being state-of-the-art technology for body composition analysis. Compared to other indirect techniques such as scales, calipers, bioimpedance, and dual-energy X-ray absorptiometry (DXA), MRI offers direct and precise measurements of the volumes of different tissue compartments and also enables quantification of diffuse fat infiltration in organs. Here, we describe a protocol for acquiring of fat–water-separated MRI data and the image postprocessing required for the quantification of several body composition biomarkers relevant for metabolic research. This protocol has successfully been used in several clinical studies and also in the large UK Biobank population study.
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| 32. |
- Borga, Magnus
(författare)
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Reinforcement Learning Using Local Adaptive Models
- 1995
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, the theory of reinforcement learning is described and its relation to learning in biological systems is discussed. Some basic issues in reinforcement learning, the credit assignment problem and perceptual aliasing, are considered. The methods of temporal difference are described. Three important design issues are discussed: information representation and system architecture, rules for improving the behaviour and rules for the reward mechanisms. The use of local adaptive models in reinforcement learning is suggested and exemplified by some experiments. This idea is behind all the work presented in this thesis. A method for learning to predict the reward called the prediction matrix memory is presented. This structure is similar to the correlation matrix memory but differs in that it is not only able to generate responses to given stimuli but also to predict the rewards in reinforcement learning. The prediction matrix memory uses the channel representation, which is also described. A dynamic binary tree structure that uses the prediction matrix memories as local adaptive models is presented. The theory of canonical correlation is described and its relation to the generalized eigenproblem is discussed. It is argued that the directions of canonical correlations can be used as linear models in the input and output spaces respectively in order to represent input and output signals that are maximally correlated. It is also argued that this is a better representation in a response generating system than, for example, principal component analysis since the energy of the signals has nothing to do with their importance for the response generation. An iterative method for finding the canonical correlations is presented. Finally, the possibility of using the canonical correlation for response generation in a reinforcement learning system is indicated.
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| 33. |
- Borga, Magnus, et al.
(författare)
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Reproducibility and repeatability of MRI-based body composition analysis
- 2020
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Ingår i: Magnetic Resonance in Medicine. - : WILEY. - 0740-3194 .- 1522-2594. ; 84:6, s. 3146-3156
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Tidskriftsartikel (refereegranskat)abstract
- Purpose There is an absence of reproducibility studies on MRI-based body composition analysis in current literature. Therefore, the aim of this study was to investigate the between-scanner reproducibility and the repeatability of a method for MRI-based body composition analysis. Methods Eighteen healthy volunteers of varying body mass index and adiposity were each scanned twice on five different 1.5T and 3T scanners from three different vendors. Two-point Dixon neck-to knee images and two additional liver scans were acquired with similar protocols. Visceral adipose tissue (VAT) volume, abdominal subcutaneous adipose tissue (ASAT) volume, thigh muscle volume, and muscle fat infiltration (MFI) in the thigh muscle were measured. Liver proton density fat fraction (PDFF) was assessed using two different methods, the scanner vendors 6-point method and an in-house 2-point method. Within-scanner test-retest repeatability and between-scanner reproducibility were calculated using analysis of variance. Results Repeatability coefficients were 13 centiliters (cl) (VAT), 24 cl (ASAT), 17 cl (total thigh muscle volume), 0.53% (MFI), and 1.27-1.37% for liver PDFF. Reproducibility coefficients were 24 cl (VAT), 42 cl (ASAT), 31 cl (total thigh muscle volume), 1.44% (MFI), and 2.37-2.40% for liver PDFF. Conclusion For all measures except MFI, the within-scanner repeatability explained much of the overall reproducibility. The two methods for measuring liver fat had similar reproducibility. This study showed that the investigated method eliminates effects due to scanner differences. The results can be used for power calculations in clinical studies or to better understand the scanner-induced variability in clinical applications.
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| 34. |
- Borga, Magnus, et al.
(författare)
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Semi-Supervised Learning of Anatomical Manifolds for Atlas-Based Segmentation of Medical Images
- 2016
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Ingår i: Proceedings of the 23rd International Conference on Pattern Recognition (ICPR). - : IEEE Computer Society. - 9781509048472 - 9781509048489 ; , s. 3146-3149
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Konferensbidrag (refereegranskat)abstract
- This paper presents a novel method for atlas-based segmentation of medical images. The method uses semi- supervised learning of a graph describing a manifold of anatom- ical variations of whole-body images, where unlabelled data are used to find a path with small deformations from the labelled atlas to the target image. The method is evaluated on 36 whole-body magnetic resonance images with manually segmented livers as ground truth. Significant improvement (p < 0.001) was obtained compared to direct atlas-based registration.
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| 35. |
- Borga, Magnus, et al.
(författare)
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Signal and Anatomical Constraints in Adaptive Filtering of fMRI Data
- 2007
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Ingår i: Biomedical Imaging: From Nano to Macro, 2007. ISBI 2007. - : IEEE. - 1424406722 ; , s. 432-435
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Konferensbidrag (refereegranskat)abstract
- An adaptive filtering method for fMRI data is presented. The method is related to bilateral filtering, but with a range filter that takes into account local similarities in signal as well as in anatomy. Performance is demonstrated on simulated and real data. It is shown that using both these similarity constraints give better performance than if only one of them is used, and clearly better than standard low-pass filtering.
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| 36. |
- Borga, Magnus, et al.
(författare)
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Validation of a Fast Method for Quantification of Intra-abdominal and Subcutaneous Adipose Tissue for Large Scale Human Studies
- 2015
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Ingår i: NMR in Biomedicine. - : John Wiley & Sons. - 1099-1492 .- 0952-3480. ; 28:12, s. 1747-1753
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Tidskriftsartikel (refereegranskat)abstract
- Central obesity is the hallmark of a number of non-inheritable disorders. The advent of imaging techniques such as magnetic resonance imaging (MRI) has allowed for a fast and accurate assessment of body fat content and distribution. However, image analysis continues to be one of the major obstacles for the use of MRI in large scale studies. In this study we assess the validity of the recently proposed fat-muscle-quantitation-system (AMRATM Profiler) for the quantification of intra-abdominal adipose tissue (IAAT) and abdominal subcutaneous adipose tissue (ASAT) from abdominal MR images. Abdominal MR images were acquired from 23 volunteers with a broad range of BMIs and analysed using SliceOmatic, the current gold-standard, and the AMRATM Profiler based on a non-rigid image registration of a library of segmented atlases. The results show that there was a highly significant correlation between the fat volumes generated by both analysis methods, (Pearson correlation r = 0.97 p<0.001), with the AMRATM Profiler analysis being significantly faster (~3 mins) than the conventional SliceOmatic approach (~40 mins). There was also excellent agreement between the methods for the quantification of IAAT (AMRA 4.73 ± 1.99 vs SliceOmatic 4.73 ± 1.75 litres, p=0.97). For the AMRATM Profiler analysis, the intra-observer coefficient of variation was 1.6 % for IAAT and 1.1 % for ASAT, the inter-observer coefficient of variation was 1.4 % for IAAT and 1.2 % for ASAT, the intra-observer correlation was 0.998 for IAAT and 0.999 for ASAT, and the inter-observer correlation was 0.999 for both IAAT and ASAT. These results indicate that precise and accurate measures of body fat content and distribution can be obtained in a fast and reliable form by the AMRATM Profiler, opening up the possibility of large-scale human phenotypic studies.
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| 37. |
- Cros, Olivier, et al.
(författare)
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Determination of the mastoid surface area and volume based on micro-CT scanning of human temporal bone : Geometrical parameters dependence on scanning resolutions
- 2016
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Ingår i: Hearing Research. - : Elsevier BV. - 0378-5955 .- 1878-5891. ; 340, s. 127-134
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Tidskriftsartikel (refereegranskat)abstract
- The mastoid air cell system (MACS) with its large complex of interconnected air cells reflects an enhanced surface area (SA) relative to its volume (V), which may indicate that the MACS is adapted to gas exchange and has a potential role in middle ear pressure regulation. Thus, these geometric parameters of the MACS have been studied by high resolution clinical CT scanning. However, the resolution of these scans is limited to a voxel size of around 0.6 mm in all dimensions, and so, the geometrical parameters are also limited. Small air cells may appear below the resolution and cannot be detected. Such air cells may contribute to a much higher SA than the V, and thus, also the SA/V ratio. More accurate parameters are important for analysis of the function of the MACS including physiological modeling.Our aim was to determine the SA, V, and SA/V ratio in MACS in human temporal bones at highest resolution by using micro-CT-scanning. Further, the influence of the resolution on these parameters was investigated by downsampling the data. Eight normally aerated temporal bones were scanned at the highest possible resolution (30-60 μm). The SA was determined using a triangular mesh fitted onto the segmented MACS. The V was determined by summing all the voxels containing air. Downsampling of the original data was applied four times by a factor of 2.The mean SA was 194 cm2, the mean V was 9 cm3, and the mean SA/V amounted to 22 cm-1. Decreasing the resolution resulted in a non-linear decrement of SA and SA/V, whereas V was mainly independent of the resolution.The current study found significantly higher SA and SA/V compared with previous studies using clinical CT scanning at lower resolutions. These findings indicate a separate role of the MACS compared with the tympanum, and the results are important for a more accurate modeling of the middle ear physiology.
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| 38. |
- Cros, Olivier, 1975-
(författare)
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Image Analysis and Visualization of the Human Mastoid Air Cell System
- 2015
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- From an engineering background, it is often believed that the human anatomy has already been fully described. Radiology has greatly contributed to understand the inside of the human body without surgical intervention. Despite great advances in clinical CT scanning, image quality is still related to a limited amount X-ray exposure for the patient safety. This limitation prevents fine anatomical structures to be visible and, more importantly, to be detected. Where such modality is of great advantage for screening patients, extracting parameters like surface area and volume implies the bone structure to be large enough in relation to the scan resolution.The mastoid, located in the temporal bone, houses an air cell system whose cells have a variation in size that can go far below current conventional clinical CT scanner resolution. Therefore, the mastoid air cell system is only partially represented on a CT scan. Any statistical analysis will be biased towards air cells of smaller size. To allow a complete representation of the mastoid air cell system, a micro-CT scanner is more adequate. Micro-CT scanning uses approximately the same amount of X-rays but for a much longer exposure time compared to what is normally allowed for patients. Human temporal bone specimens are therefore necessary when using such scanning method. Where the conventional clinical CT scanner lacks level of minutes details, micro-CT scanning provides an overwhelming amount of fine details.Prior to any image analysis of medical data, visualization of the data is often needed to learn how to extract the structures of interest for further processing. Visualization of micro-CT scans is of no exception. Due to the high resolution nature of the data, visualization of such data not only requires modern and powerful computers, but also necessitates a tremendous amount of time to adjust the hiding of irrelevant structures, to find the correct orientation, while emphasising the structure of interest. Once the quality of the data has been assessed, and a strategy for the image processing has been decided, the image processing can start, to in turn extract metrics such as the surface area or volume and draw statistics from it. The temporal bone being one of the most complex in the human body, visualization of micro-CT scanning of this bone awakens the curiosity of the experimenter, especially with the correct visualization settings.This thesis first presents a statistical analysis determining the surface area to volume ratio of the mastoid air cell system of human temporal bone, from micro-CT scanning using methods previously applied for conventional clinical CT scannings. The study compared current resul s with previous studies, with successive downsampling the data down to a resolution found in conventional clinical CT scanning. The results from the statistical analysis showed that all the small mastoid air cells, that cannot be detected in conventional clinical CT scans, do heavily contribute to the estimation of the surface area, and in consequence to the estimation of the surface area to volume ratio by a factor of about 2.6. Such a result further strengthens the idea of the mastoid to play an active role in pressure regulation and gas exchange.Discovery of micro-channels through specific use of a non-traditional transfer function was then reported, where a qualitative and a quantitative preanalysis was performed are described. To gain more knowledge about these micro-channels, a local structure tensor analysis was applied where structures are described in terms of planar, tubular, or isotropic structures. The results from this structural tensor analysis, also reported in this thesis, suggest these micro-channels to potentially be part of a more complex framework, which hypothetically would provide a separate blood supply for the mucosa lining the mastoid air cell system.
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| 39. |
- Cros, Olivier, et al.
(författare)
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Mastoid structural properties determined by imaging analysis of high resolution CT-scanning
- 2010
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Ingår i: Hearing Research. - : Elsevier. - 0378-5955 .- 1878-5891. ; 263:1-2, s. 242-243
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Tidskriftsartikel (refereegranskat)abstract
- Hypothesis: The structure of the mastoid air cells can be described by quantitative imaging analysis of high-resolution CT-scans, which may contribute to understand its function in normal and pathological ears. Background: Negative middle ear pressure is a common factor in middle ear diseases resulting from an imbalance between mastoid gas exchange and Eustachian tube function. While the Eustachian tube function has been the main focus of research, more recent studies indicate that the mastoid may play an active role in pressure regulation. The mastoid structure with numerous air cells reflects a large area to volume ratio (AV-ratio) adapted to efficient gas exchange. Imaging analysis applied to high resolution CT-scanning can describe quantitative measures, which may reveal important information about mastoid function and its role in healthy and diseased ears. Materials and methods: Quantitative analysis was performed on a series of unselected high resolution CT-scans (voxel size: 0.29 _ 0.29 _ 0.625 mm) from 36 ears in 24 patients. Area and volume were determined using Cavalieri’s method, i.e. by summing cross-sectional areas. The AV-ratio was computed for each scan. Results: Mean area was 69 cm2 (range: 23–134cm2), mean volume was 4 cm3 (range: 1.3–10.8 cm3), and mean AV-ratio was 16 cm-1 (range: 11.2–21.0 cm-1). The area correlated linearly to the volume by A = 17.2*V-0.2. Conclusion: The area and volume values corresponded with previous studies, and the additional AV-ratio reflected the functional properties of the mastoid in terms of capability for gas exchange. Due to a series of similarities between structure and function of the lungs and mastoid, it seems likely to propose a tree-structure of dividing mastoid cells. In respiratory research, analysis describing the dimensions of series of bronchi generations has been applied, and based on current results; our aim of future research is to establish similar details of mastoid tree-structure. Funding source: Various private Danish funds.
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| 40. |
- Cros, Olivier, et al.
(författare)
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Micro-channels in the mastoid anatomy. Indications of a separate blood supply of the air cell system mucosa by micro-CT scanning
- 2013
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Ingår i: Hearing Research. - : Elsevier. - 0378-5955 .- 1878-5891. ; 301, s. 60-65
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Tidskriftsartikel (refereegranskat)abstract
- The mastoid air cell system has traditionally been considered to have a passive role in gas exchange and pressure regulation of the middle ear possibly with some acoustic function. However, more evidence has focused on the mucosa of the mastoid, which may play a more active role in regulation of middle ear pressure.In this study we have applied micro-CT scanning on a series of three human temporal bones. This approach greatly enhances the resolution (40–60 μm), so that we have discovered anatomical details, which has not been reported earlier. Thus, qualitative analysis using volume rendering has demonstrated notable micro-channels connecting the surface of the compact bone directly to the mastoid air cells as well as forming a network of connections between the air cells. Quantitative analysis on 2D slices was employed to determine the average diameter of these micro-channels (158 μm; range = 40–440 μm) as well as their density at a localized area (average = 75 cm−2; range = 64–97 cm−2).These channels are hypothesized to contain a separate vascular supply for the mastoid mucosa. However, future studies of the histological structure of the micro-channels are warranted to confirm the hypothesis. Studies on the mastoid mucosa and its blood supply may improve our knowledge of its physiological properties, which may have important implications for our understanding of the pressure regulation of the middle ear.
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