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  • 101.
    Borga, Magnus
    et al.
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    West, Janne
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Faculty of Medicine and Health Sciences.
    Bell, Jimmy
    Westminster University, London, UK.
    Harvey, Nicholas
    University of Southampton, IK.
    Romu, Thobias
    Linköping University, Department of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Heymsfield, Steven
    Pennington Biomedical Research Center, Baton Rouge, LA, US.
    Dahlqvist Leinhard, Olof
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV). Region Östergötland, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Radiation Physics. Advanced MR Analytics AB, Linköping, Sweden.
    Advanced body composition assessment: From body mass index to body composition profiling2018In: Journal of Investigative Medicine, ISSN 1081-5589, E-ISSN 1708-8267, Vol. 66, p. 887-895Article, review/survey (Refereed)
    Abstract [en]

    This paper gives a brief overview of common non-invasive techniques for body composition analysis and a more in-depth review of a body composition assessment method based on fat-referenced quantitative magnetic resonance imaging (MRI). Earlier published studies of this method are summarized, and a previously un-published validation study, based on 4.753 subjects from the UK Biobank imaging cohort, comparing the quantitative MRI method with dual-energy x-ray absorptiometry (DXA) is presented. For whole-body measurements of adipose tissue (AT) or fat and lean tissue (LT), DXA and quantitative MRI show excellent agreement with linear correlation of 0.99 and 0.97, and coefficient of variation (CV) of 4.5 % and 4.6 % for fat (computed from AT) and lean tissue respectively, but the agreement was found significantly lower for visceral adipose tissue, with a CV of more than 20 %. The additional ability of MRI to also measure muscle volumes, muscle AT infiltration and ectopic fat in combination with rapid scanning protocols and efficient image analysis tools make quantitative MRI a powerful tool for advanced body composition assessment. 

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    Advanced body composition assessment: From body mass index to body composition profiling
  • 102.
    Brandberg, Joakim
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Janerot Sjöberg, Birgitta
    Linköping University, Department of Medicine and Care, Clinical Physiology. Linköping University, Faculty of Health Sciences.
    Ask, Per
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Increased accuracy of echocardiographic measurement of flow using automated spherical integration of multiple plane velocity vectors1999In: Ultrasound in Medicine and Biology, ISSN 0301-5629, E-ISSN 1879-291X, Vol. 25, no 2, p. 249-257Article in journal (Refereed)
    Abstract [en]

    The calculation of blood flow in the heart by surface integration of velocity vectors (SIVV) using Doppler ultrasound is independent of the angle. Flow is normally calculated from velocity in a spherical thick shell with its center located at the ultrasound transducer. In a numerical simulation, we have shown that the ratio between minor and major axes of an elliptic flow area substantially influences the accuracy of the estimation of flow in a single scan plane. The accuracy of flow measurements by SIVV can be improved by calculating the mean of the values from more than one scan plane. We have produced an automated computer program that includes an antialiasing procedure. We confirmed an improvement of flow measurements in a pulsatile hydraulic flow model, the 95% confidence interval for single estimations being reduced from 20% to 10% (p < 0.05) using the newly developed software. We think that the SIVV method has important implications for clinical transthoracic echocardiography.

  • 103.
    Brandl, Miriam B
    et al.
    School of Engineering and Information Technology, The University of New South Wales, Canberra, Australia .
    Beck, Dominik
    School of Engineering and Information Technology, The University of New South Wales, Canberra, Australia .
    Pham, Tuan D
    School of Engineering and Information Technology, The University of New South Wales, Canberra, Australia .
    Application of Fuzzy c-Means and Joint-Feature-Clustering to Detect Redundancies of Image-Features in Drug Combinations Studies of Breast Cancer2011Conference paper (Refereed)
    Abstract [en]

    The high dimensionality of image-based dataset can be a drawback for classification accuracy. In this study, we propose the application of fuzzy c-means clustering, cluster validity indices and the notation of a joint-feature-clustering matrix to find redundancies of image-features. The introduced matrix indicates how frequently features are grouped in a mutual cluster. The resulting information can be used to find data-derived feature prototypes with a common biological meaning, reduce data storage as well as computation times and improve the classification accuracy.

  • 104. Order onlineBuy this publication >>
    Brun, Anders
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Manifolds in Image Science and Visualization2007Doctoral thesis, monograph (Other academic)
    Abstract [en]

    A Riemannian manifold is a mathematical concept that generalizes curved surfaces to higher dimensions, giving a precise meaning to concepts like angle, length, area, volume and curvature. A glimpse of the consequences of a non-flat geometry is given on the sphere, where the shortest path between two points – a geodesic – is along a great circle. Different from Euclidean space, the angle sum of geodesic triangles on the sphere is always larger than 180 degrees.

    Signals and data found in applied research are sometimes naturally described by such curved spaces. This dissertation presents basic research and tools for the analysis, processing and visualization of such manifold-valued data, with a particular emphasis on future applications in medical imaging and visualization.

    Two-dimensional manifolds, i.e. surfaces, enter naturally into the geometric modelling of anatomical entities, such as the human brain cortex and the colon. In advanced algorithms for processing of images obtained from computed tomography (CT) and ultrasound imaging (US), images themselves and derived local structure tensor fields may be interpreted as two- or three-dimensional manifolds. In diffusion tensor magnetic resonance imaging (DT-MRI), the natural description of diffusion in the human body is a second-order tensor field, which can be related to the metric of a manifold. A final example is the analysis of shape variations of anatomical entities, e.g. the lateral ventricles in the brain, within a population by describing the set of all possible shapes as a manifold.

    Work presented in this dissertation include: Probabilistic interpretation of intrinsic and extrinsic means in manifolds. A Bayesian approach to filtering of vector data, removing noise from sampled manifolds and signals. Principles for the storage of tensor field data and learning a natural metric for empirical data.

    The main contribution is a novel class of algorithms called LogMaps, for the numerical estimation of logp (x) from empirical data sampled from a low-dimensional manifold or geometric model embedded in Euclidean space. The logp (x) function has been used extensively in the literature for processing data in manifolds, including applications in medical imaging such as shape analysis. However, previous approaches have been limited to manifolds where closed form expressions of logp (x) have been known. The introduction of the LogMap framework allows for a generalization of the previous methods. The application of LogMaps to texture mapping, tensor field visualization, medial locus estimation and exploratory data analysis is also presented.

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  • 105.
    Brynolfsson, Patrik
    Linköping University, Department of Medicine and Health Sciences, Radiation Physics. Linköping University, Center for Medical Image Science and Visualization, CMIV.
    Using radial k-space sampling and temporal filters in MRI to improve temporal resolution2010Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In this master thesis methods for increasing temporal resolution when reconstructing radially sampled MRI data have been developed and evaluated. This has been done in two steps; first the order in which data is sampled in k-space has been optimized, and second; temporal filters have been developed in order to utilize the high sampling density in central regions of k-space as a result of the polar sampling geometry to increase temporal resolution while maintaining image quality.By properly designing the temporal filters the temporal resolution is increased by a factor 3–20 depending on other variables such as imageresolution and the size of the time varying areas in the image. The results are obtained from simulated raw data and subsequent reconstruction. The next step should be to acquire and reconstruct raw data to confirm the results.

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    FULLTEXT01
  • 106.
    Budde, Kiran Kumar
    Linköping University, Department of Electrical Engineering, Computer Vision.
    A Matlab Toolbox for fMRI Data Analysis: Detection, Estimation and Brain Connectivity2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Functional Magnetic Resonance Imaging (fMRI) is one of the best techniques for neuroimaging and has revolutionized the way to understand the brain functions. It measures the changes in the blood oxygen level-dependent (BOLD) signal which is related to the neuronal activity. Complexity of the data, presence of different types of noises and the massive amount of data makes the fMRI data analysis a challenging one. It demands efficient signal processing and statistical analysis methods.  The inference of the analysis is used by the physicians, neurologists and researchers for better understanding of the brain functions.

         The purpose of this study is to design a toolbox for fMRI data analysis. It includes methods to detect the brain activity maps, estimation of the hemodynamic response (HDR) and the connectivity of the brain structures. This toolbox provides methods for detection of activated brain regions measured with Bayesian estimator. Results are compared with the conventional methods such as t-test, ordinary least squares (OLS) and weighted least squares (WLS). Brain activation and HDR are estimated with linear adaptive model and nonlinear method based on radial basis function (RBF) neural network. Nonlinear autoregressive with exogenous inputs (NARX) neural network is developed to model the dynamics of the fMRI data.  This toolbox also provides methods to brain connectivity such as functional connectivity and effective connectivity.  These methods are examined on simulated and real fMRI datasets.

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    A Matlab Toolbox for fMRI Data Analysis: Detection, Estimation and Brain Connectivity
  • 107.
    Bujack, Roxana
    et al.
    Leipzig University, Leipzig, Germany.
    Hotz, Ingrid
    Zuse Institute Berlin, Germany.
    Scheuermann, Gerik
    Leipzig University, Leipzig, Germany.
    Hitzer, Eckhard
    International Christian University, Tokyo, Japan.
    Moment Invariants for 2D Flow Fields Using Normalization in Detail2015In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 21, no 8, p. 916-929Article in journal (Refereed)
    Abstract [en]

    The analysis of 2D flow data is often guided by the search for characteristic structures with semantic meaning. One way to approach this question is to identify structures of interest by a human observer, with the goal of finding similar structures in the same or other datasets. The major challenges related to this task are to specify the notion of similarity and define respective pattern descriptors. While the descriptors should be invariant to certain transformations, such as rotation and scaling, they should provide a similarity measure with respect to other transformations, such as deformations. In this paper, we propose to use moment invariants as pattern descriptors for flow fields. Moment invariants are one of the most popular techniques for the description of objects in the field of image recognition. They have recently also been applied to identify 2D vector patterns limited to the directional properties of flow fields. Moreover, we discuss which transformations should be considered for the application to flow analysis. In contrast to previous work, we follow the intuitive approach of moment normalization, which results in a complete and independent set of translation, rotation, and scaling invariant flow field descriptors. They also allow to distinguish flow features with different velocity profiles. We apply the moment invariants in a pattern recognition algorithm to a real world dataset and show that the theoretical results can be extended to discrete functions in a robust way.

  • 108. Order onlineBuy this publication >>
    Bustamante, Mariana
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Automated Assessment of Blood Flow in the Cardiovascular System Using 4D Flow MRI2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Medical image analysis focuses on the extraction of meaningful information from medical images in order to facilitate clinical assessment, diagnostics and treatment. Image processing techniques have gradually become an essential part of the modern health care system, a consequence of the continuous technological improvements and the availability of a variety of medical imaging techniques.

    Magnetic Resonance Imaging (MRI) is an imaging technique that stands out as non-invasive, highly versatile, and capable of generating high quality images without the use of ionizing radiation. MRI is frequently performed in the clinical setting to assess the morphology and function of the heart and vessels. When focusing on the cardiovascular system, blood flow visualization and quantification is essential in order to fully understand and identify related pathologies. Among the variety of MR techniques available for cardiac imaging, 4D Flow MRI allows for full three-dimensional spatial coverage over time, also including three-directional velocity information. It is a very powerful technique that can be used for retrospective analysis of blood flow dynamics at any location in the acquired volume.

    In the clinical routine, however, flow analysis is typically done using two-dimensional imaging methods. This can be explained by their shorter acquisition times, higher in-plane spatial resolution and signal-to-noise ratio, and their relatively simpler post-processing requirements when compared to 4D Flow MRI. The extraction of useful knowledge from 4D Flow MR data is especially challenging due to the large amount of information included in these images, and typically requires substantial user interaction.

    This thesis aims to develop and evaluate techniques that facilitate the post-processing of thoracic 4D Flow MRI by automating the steps necessary to obtain hemodynamic parameters of interest from the data. The proposed methods require little to no user interaction, are fairly quick, make effective use of the information available in the four-dimensional images, and can easily be applied to sizable groups of data.The addition of the proposed techniques to the current pipeline of 4D Flow MRI analysis simplifies and expedites the assessment of these images, thus bringing them closer to the clinical routine.

    List of papers
    1. Improving left ventricular segmentation in four-dimensional flow MRI using intramodality image registration for cardiac blood flow analysis
    Open this publication in new window or tab >>Improving left ventricular segmentation in four-dimensional flow MRI using intramodality image registration for cardiac blood flow analysis
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    2018 (English)In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 79, no 1, p. 554-560Article in journal (Refereed) Published
    Abstract [en]

    PurposeAssessment of blood flow in the left ventricle using four-dimensional flow MRI requires accurate left ventricle segmentation that is often hampered by the low contrast between blood and the myocardium. The purpose of this work is to improve left-ventricular segmentation in four-dimensional flow MRI for reliable blood flow analysis. MethodThe left ventricle segmentations are first obtained using morphological cine-MRI with better in-plane resolution and contrast, and then aligned to four-dimensional flow MRI data. This alignment is, however, not trivial due to inter-slice misalignment errors caused by patient motion and respiratory drift during breath-hold based cine-MRI acquisition. A robust image registration based framework is proposed to mitigate such errors automatically. Data from 20 subjects, including healthy volunteers and patients, was used to evaluate its geometric accuracy and impact on blood flow analysis. ResultsHigh spatial correspondence was observed between manually and automatically aligned segmentations, and the improvements in alignment compared to uncorrected segmentations were significant (Pamp;lt;0.01). Blood flow analysis from manual and automatically corrected segmentations did not differ significantly (Pamp;gt;0.05). ConclusionOur results demonstrate the efficacy of the proposed approach in improving left-ventricular segmentation in four-dimensional flow MRI, and its potential for reliable blood flow analysis. Magn Reson Med 79:554-560, 2018. (c) 2017 International Society for Magnetic Resonance in Medicine.

    Place, publisher, year, edition, pages
    WILEY, 2018
    Keywords
    four-dimensional flow MRI; image registration; blood flow analysis; cardiology; MRI; 4D flow MRI; image registration; blood flow analysis; cardiology; MRI
    National Category
    Medical Image Processing
    Identifiers
    urn:nbn:se:liu:diva-143887 (URN)10.1002/mrm.26674 (DOI)000417926300054 ()28303611 (PubMedID)
    Note

    Funding Agencies|ERC [310612]; 310612; Grant sponsor: Vetenskapsradet [621-2014-6191]; Hjart-Lungfonden [20140398]; Knut och Alice Wallenbergs Stiftelse [KAW 2013.0076]

    Available from: 2017-12-29 Created: 2017-12-29 Last updated: 2018-03-22
    2. Atlas-based analysis of 4D flow CMR: Automated vessel segmentation and flow quantification
    Open this publication in new window or tab >>Atlas-based analysis of 4D flow CMR: Automated vessel segmentation and flow quantification
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    2015 (English)In: Journal of Cardiovascular Magnetic Resonance, ISSN 1097-6647, E-ISSN 1532-429X, Vol. 17, no 87Article in journal (Refereed) Published
    Abstract [en]

    Background: Flow volume quantification in the great thoracic vessels is used in the assessment of several cardiovascular diseases. Clinically, it is often based on semi-automatic segmentation of a vessel throughout the cardiac cycle in 2D cine phase-contrast Cardiovascular Magnetic Resonance (CMR) images. Three-dimensional (3D), time-resolved phase-contrast CMR with three-directional velocity encoding (4D flow CMR) permits assessment of net flow volumes and flow patterns retrospectively at any location in a time-resolved 3D volume. However, analysis of these datasets can be demanding. The aim of this study is to develop and evaluate a fully automatic method for segmentation and analysis of 4D flow CMR data of the great thoracic vessels. Methods: The proposed method utilizes atlas-based segmentation to segment the great thoracic vessels in systole, and registration between different time frames of the cardiac cycle in order to segment these vessels over time. Additionally, net flow volumes are calculated automatically at locations of interest. The method was applied on 4D flow CMR datasets obtained from 11 healthy volunteers and 10 patients with heart failure. Evaluation of the method was performed visually, and by comparison of net flow volumes in the ascending aorta obtained automatically (using the proposed method), and semi-automatically. Further evaluation was done by comparison of net flow volumes obtained automatically at different locations in the aorta, pulmonary artery, and caval veins. Results: Visual evaluation of the generated segmentations resulted in good outcomes for all the major vessels in all but one dataset. The comparison between automatically and semi-automatically obtained net flow volumes in the ascending aorta resulted in very high correlation (r(2) = 0.926). Moreover, comparison of the net flow volumes obtained automatically in other vessel locations also produced high correlations where expected: pulmonary trunk vs. proximal ascending aorta (r(2) = 0.955), pulmonary trunk vs. pulmonary branches (r(2) = 0.808), and pulmonary trunk vs. caval veins (r(2) = 0.906). Conclusions: The proposed method allows for automatic analysis of 4D flow CMR data, including vessel segmentation, assessment of flow volumes at locations of interest, and 4D flow visualization. This constitutes an important step towards facilitating the clinical utility of 4D flow CMR.

    Place, publisher, year, edition, pages
    BIOMED CENTRAL LTD, 2015
    Keywords
    4D flow cardiovascular magnetic resonance (4D flow CMR); Flow volume; Image segmentation; Image registration; Phase contrast
    National Category
    Clinical Medicine
    Identifiers
    urn:nbn:se:liu:diva-122197 (URN)10.1186/s12968-015-0190-5 (DOI)000362164100002 ()26438074 (PubMedID)
    Note

    Funding Agencies|Swedish Heart and Lung foundation; Swedish Research Council; European Research Council (HEART4FLOW) [310612]

    Available from: 2015-10-26 Created: 2015-10-23 Last updated: 2018-03-22
    3. Improving visualization of 4D flow cardiovascular magnetic resonance with four-dimensional angiographic data: generation of a 4D phase-contrast magnetic resonance CardioAngiography (4D PC-MRCA)
    Open this publication in new window or tab >>Improving visualization of 4D flow cardiovascular magnetic resonance with four-dimensional angiographic data: generation of a 4D phase-contrast magnetic resonance CardioAngiography (4D PC-MRCA)
    2017 (English)In: Journal of Cardiovascular Magnetic Resonance, ISSN 1097-6647, E-ISSN 1532-429X, Vol. 19, article id 47Article in journal (Refereed) Published
    Abstract [en]

    Magnetic Resonance Angiography (MRA) and Phase-Contrast MRA (PC-MRA) approaches used for assessment of cardiovascular morphology typically result in data containing information from the entire cardiac cycle combined into one 2D or 3D image. Information specific to each timeframe of the cardiac cycle is, however, lost in this process. This study proposes a novel technique, called Phase-Contrast Magnetic Resonance CardioAngiography (4D PC-MRCA), that utilizes the full potential of 4D Flow CMR when generating temporally resolved PC-MRA data to improve visualization of the heart and major vessels throughout the cardiac cycle. Using non-rigid registration between the timeframes of the 4D Flow CMR acquisition, the technique concentrates information from the entire cardiac cycle into an angiographic dataset at one specific timeframe, taking movement over the cardiac cycle into account. Registration between the timeframes is used once more to generate a time-resolved angiography. The method was evaluated in ten healthy volunteers. Visual comparison of the 4D PC-MRCAs versus PC-MRAs generated from 4D Flow CMR using the traditional approach was performed by two observers using Maximum Intensity Projections (MIPs). The 4D PC-MRCAs resulted in better visibility of the main anatomical regions of the cardiovascular system, especially where cardiac or vessel motion was present. The proposed method represents an improvement over previous PC-MRA generation techniques that rely on 4D Flow CMR, as it effectively utilizes all the information available in the acquisition. The 4D PC-MRCA can be used to visualize the motion of the heart and major vessels throughout the entire cardiac cycle.

    Place, publisher, year, edition, pages
    BIOMED CENTRAL LTD, 2017
    Keywords
    Computer-Assisted Image Analysis; 4D flow cardiovascular magnetic resonance (4D flow CMR); Phase-Contrast Magnetic Resonance Angiography (PC-MRA)
    National Category
    Radiology, Nuclear Medicine and Medical Imaging
    Identifiers
    urn:nbn:se:liu:diva-139277 (URN)10.1186/s12968-017-0360-8 (DOI)000404063800001 ()28645326 (PubMedID)
    Note

    Funding Agencies|European Research Council [310612]; Swedish Heart and Lung foundation [20140398]; Swedish Research Council [621-2014-6191]

    Available from: 2017-07-07 Created: 2017-07-07 Last updated: 2018-03-22
    4. Creating Hemodynamic Atlases of Cardiac 4D Flow MRI
    Open this publication in new window or tab >>Creating Hemodynamic Atlases of Cardiac 4D Flow MRI
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    2017 (English)In: Journal of Magnetic Resonance Imaging, ISSN 1053-1807, E-ISSN 1522-2586, Vol. 46, no 5, p. 1389-1399Article in journal (Refereed) Published
    Abstract [en]

    Purpose: Hemodynamic atlases can add to the pathophysiological understanding of cardiac diseases. This study proposes a method to create hemodynamic atlases using 4D Flow magnetic resonance imaging (MRI). The method is demonstrated for kinetic energy (KE) and helicity density (Hd). Materials and Methods: Thirteen healthy subjects underwent 4D Flow MRI at 3T. Phase-contrast magnetic resonance cardioangiographies (PC-MRCAs) and an average heart were created and segmented. The PC-MRCAs, KE, and Hd were nonrigidly registered to the average heart to create atlases. The method was compared with 1) rigid, 2) affine registration of the PC-MRCAs, and 3) affine registration of segmentations. The peak and mean KE and Hd before and after registration were calculated to evaluate interpolation error due to nonrigid registration. Results: The segmentations deformed using nonrigid registration overlapped (median: 92.3%) more than rigid (23.1%, P amp;lt; 0.001), and affine registration of PC-MRCAs (38.5%, P amp;lt; 0.001) and affine registration of segmentations (61.5%, P amp;lt; 0.001). The peak KE was 4.9 mJ using the proposed method and affine registration of segmentations (P50.91), 3.5 mJ using rigid registration (P amp;lt; 0.001), and 4.2 mJ using affine registration of the PC-MRCAs (P amp;lt; 0.001). The mean KE was 1.1 mJ using the proposed method, 0.8 mJ using rigid registration (P amp;lt; 0.001), 0.9 mJ using affine registration of the PC-MRCAs (P amp;lt; 0.001), and 1.0 mJ using affine registration of segmentations (P50.028). The interpolation error was 5.262.6% at mid-systole, 2.863.8% at early diastole for peak KE; 9.669.3% at mid-systole, 4.064.6% at early diastole, and 4.964.6% at late diastole for peak Hd. The mean KE and Hd were not affected by interpolation. Conclusion: Hemodynamic atlases can be obtained with minimal user interaction using nonrigid registration of 4D Flow MRI. Level of Evidence: 2 Technical Efficacy: Stage 1

    Place, publisher, year, edition, pages
    WILEY, 2017
    National Category
    Medical Image Processing
    Identifiers
    urn:nbn:se:liu:diva-142968 (URN)10.1002/jmri.25691 (DOI)000412894800015 ()28295788 (PubMedID)
    Note

    Funding Agencies|ERC [Heart4flow, 310612]; Swedish Research Council [621-2014-6191]; Swedish Heart and Lung Foundation [20140398]

    Available from: 2017-11-13 Created: 2017-11-13 Last updated: 2018-03-22
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    Automated Assessment of Blood Flow in the Cardiovascular System Using 4D Flow MRI
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  • 109.
    Bustamante, Mariana
    et al.
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Gupta, Vikas
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Forsberg, Daniel
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Sectra, Linköping, Sweden.
    Carlhäll, Carljohan
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Clinical Physiology in Linköping.
    Engvall, Jan
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Clinical Physiology in Linköping.
    Ebbers, Tino
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Clinical Physiology in Linköping. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Automated multi-atlas segmentation of cardiac 4D flow MRI2018In: Medical Image Analysis, ISSN 1361-8415, E-ISSN 1361-8423, Vol. 49, p. 128-140Article in journal (Refereed)
    Abstract [en]

    Four-dimensional (4D) flow magnetic resonance imaging (4D Flow MRI) enables acquisition of time-resolved three-directional velocity data in the entire heart and all major thoracic vessels. The segmentation of these tissues is typically performed using semi-automatic methods. Some of which primarily rely on the velocity data and result in a segmentation of the vessels only during the systolic phases. Other methods, mostly applied on the heart, rely on separately acquired balanced Steady State Free Precession (b-SSFP) MR images, after which the segmentations are superimposed on the 4D Flow MRI. While b-SSFP images typically cover the whole cardiac cycle and have good contrast, they suffer from a number of problems, such as large slice thickness, limited coverage of the cardiac anatomy, and being prone to displacement errors caused by respiratory motion. To address these limitations we propose a multi-atlas segmentation method, which relies only on 4D Flow MRI data, to automatically generate four-dimensional segmentations that include the entire thoracic cardiovascular system present in these datasets. The approach was evaluated on 4D Flow MR datasets from a cohort of 27 healthy volunteers and 83 patients with mildly impaired systolic left-ventricular function. Comparison of manual and automatic segmentations of the cardiac chambers at end-systolic and end-diastolic timeframes showed agreements comparable to those previously reported for automatic segmentation methods of b-SSFP MR images. Furthermore, automatic segmentation of the entire thoracic cardiovascular system improves visualization of 4D Flow MRI and facilitates computation of hemodynamic parameters.

    The full text will be freely available from 2020-08-13 11:32
  • 110.
    Bäckström, Martin
    Linköping University, Department of Biomedical Engineering.
    Discrimination between healthy and cancerous lungs with the use of an electronic nose2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Lung cancer is one of the most serious and common cancer types of today, with very uncomfortable and potentially cumbersome diagnostic techniques in x-ray, CT, CT-PET scans, bronchoscopies and biopsies. Completing all these steps can also take a long time and be time consuming for hospital staff. So finding a new safer and faster technique to diagnose cancer would be of great benefit.

    The objectives of this pilot study is to create an effective data storage system that can be scaled for larger data sets in a later study. The aim was also to see whether a E-nose can be used to find the differences in smell-prints from a healthy lung and a cancerous lung. As well as seeing if the E-nose can distinguish samples drawn from the lungs from exhaled air samples.

    Samples were taken on patients by the staff at ”Lung kliniken” at Link¨oping University Hospital during a bronchoscopy on patients with one-sided lung cancer. These samples were then analyzed by the E-nose which sensory response is later used to test the classification system that uses a mix of Principal Component Analysis (PCA) and K-Nearest Neighbour (KNN). Using a k = 7, the system was able to correctly classify 60 % of the samples when comparing cancerous and healthy lung samples. Comparing exhaled, healthy and cancerous samples the accuracy was calculated to 55.56 %. Comparing all lung samples against exhaled samples the accuracy was 86.67 %

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  • 111.
    Cardemil, Carina
    et al.
    Department of Biomaterials, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden, Department of Oral and Maxillofacial Surgery, Örebro University Hospital, Örebro, Sweden, BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, Gothenburg, Sweden .
    Elgali, Ibrahim
    Department of Biomaterials, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden, BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, Gothenburg, Sweden.
    Xia, Wei
    Applied Materials Science, Department of Engineering Sciences, Uppsala University, Uppsala, Sweden, BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, Gothenburg, Sweden.
    Emanuelsson, Lena
    Department of Biomaterials, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden, BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, Gothenburg, Sweden.
    Norlindh, Birgitta
    Department of Biomaterials, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden, BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, Gothenburg, Sweden.
    Omar, Omar
    Department of Biomaterials, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden, BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, Gothenburg, Sweden.
    Thomsen, Peter
    Department of Biomaterials, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden, BIOMATCELL VINN Excellence Center of Biomaterials and Cell Therapy, Gothenburg, Sweden .
    Strontium-doped calcium phosphate and hydroxyapatite granules promote different inflammatory and bone remodelling responses in normal and ovariectomised rats2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 12, article id e84932Article in journal (Refereed)
    Abstract [en]

    The healing of bone defects may be hindered by systemic conditions such as osteoporosis. Calcium phosphates, with or without ion substitutions, may provide advantages for bone augmentation. However, the mechanism of bone formation with these materials is unclear. The aim of this study was to evaluate the healing process in bone defects implanted with hydroxyapatite (HA) or strontium-doped calcium phosphate (SCP) granules, in non-ovariectomised (non-OVX) and ovariectomised (OVX) rats. After 0 (baseline), six and 28d, bone samples were harvested for gene expression analysis, histology and histomorphometry. Tumour necrosis factor-α (TNF-α), at six days, was higher in the HA, in non-OVX and OVX, whereas interleukin-6 (IL-6), at six and 28d, was higher in SCP, but only in non-OVX. Both materials produced a similar expression of the receptor activator of nuclear factor kappa-B ligand (RANKL). Higher expression of osteoclastic markers, calcitonin receptor (CR) and cathepsin K (CatK), were detected in the HA group, irrespective of non-OVX or OVX. The overall bone formation was comparable between HA and SCP, but with topological differences. The bone area was higher in the defect centre of the HA group, mainly in the OVX, and in the defect periphery of the SCP group, in both non-OVX and OVX. It is concluded that HA and SCP granules result in comparable bone formation in trabecular bone defects. As judged by gene expression and histological analyses, the two materials induced different inflammatory and bone remodelling responses. The modulatory effects are associated with differences in the spatial distribution of the newly formed bone.

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    Strontium-doped calcium phosphate and hydroxyapatite granules promote different inflammatory and bone remodelling responses in normal and ovariectomised rats
  • 112.
    Cederberg, Erik
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Center for Medical Image Science and Visualization, CMIV.
    Adipose tissue segmentation in whole-body MRI2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Adipose tissue volume and distribution is related to metabolic diseases such as diabetes and atherosclerosis. This relationship is in focus for much research, much due to a worldwide increase in obesity. It is in many cases of interest to calculate the amount of adipose tissue in different compartments within the body. Commonly used methods are however prone to introduce errors due to partial volume effects.

    Previous studies have successfully segmented three adipose tissue compartments from abdominal two-point Dixon fat-water MRI volumes using Morphon registration and atlas segmentation. This thesis extends upon the previous work by enabling segmentation of whole-body MRI volumes and by improving the registration with the use of both fat and water data. Possible methods for bone marrow segmentation are also tested and evaluated.

    The methods presented seem to be sufficient for creating whole-body volumes from a set of smaller volumes. The adipose tissue segmentation was adequate for subjects with relatively small volumes of adipose tissue, whereas segmentation of subjects with large amounts of adipose tissue require further improvement. Of the evaluated methods for bone marrow segmentation one seemed to perform adequately on all the tested datasets. Due to the few datasets available for testing it was not possible to draw any general conclusions as to how well the presented methods perform.

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  • 113.
    Cedersund, Gunnar
    et al.
    Linköping University, Department of Electrical Engineering. Linköping University, The Institute of Technology.
    Knudsen, C.
    Technical University of Denmark.
    Improved parameter estimation for systems with an experimentally located Hopf bifurcation2005In: IEE Proceedings - Systems Biology, ISSN 1741-2471, E-ISSN 1741-248X, Vol. 152, no 3, p. 161-168Article in journal (Refereed)
    Abstract [en]

    When performing system identification, we have two sources of information: experimental data and prior knowledge. Many cell-biological systems are oscillating, and sometimes we know an input where the system reaches a Hopf bifurcation. This is the case, for example, for glycolysis in yeast cells and for the Belousov-Zhabotinsky reaction, and for both of these systems there exist significant numbers of quenching data, ideal for system identification. We present a method that includes prior knowledge of the location of a Hopf bifurcation in estimation based on time-series. The main contribution is a reformulation of the prior knowledge into the standard formulation of a constrained optimisation problem. This formulation allows for any of the standard methods to be applied, including all the theories regarding the methods properties. The reformulation is carried out through an over-parametrisation of the original problem. The over-parametrisation allows for extra constraints to be formed, and the net effect is a reduction of the search space. A method that can solve the new formulation of the problem is presented, and the advantage of adding the prior knowledge is demonstrated on the Brusselator.

  • 114.
    Cervin, Ida
    et al.
    Sectra AB, Chalmers University of Technology, Sectra AB, Gothenburg, Sweden.
    Molin, Jesper
    Center for Medical Image Science and Visualization, Chalmers University of Technology, Sectra AB, Gothenburg, Sweden.
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Improving the creation and reporting of structured findings during digital pathology review2016In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 7, no 1, p. 32-32Article in journal (Refereed)
    Abstract [en]

    Background: Today, pathology reporting consists of many separate tasks, carried out by multiple people. Common tasks include dictation during case review, transcription, verification of the transcription, report distribution, and report the key findings to follow-up registries. Introduction of digital workstations makes it possible to remove some of these tasks and simplify others. This study describes the work presented at the Nordic Symposium on Digital Pathology 2015, in Linköping, Sweden. Methods: We explored the possibility to have a digital tool that simplifies image review by assisting note-taking, and with minimal extra effort, populates a structured report. Thus, our prototype sees reporting as an activity interleaved with image review rather than a separate final step. We created an interface to collect, sort, and display findings for the most common reporting needs, such as tumor size, grading, and scoring. Results: The interface was designed to reduce the need to retain partial findings in the head or on paper, while at the same time be structured enough to support automatic extraction of key findings for follow-up registry reporting. The final prototype was evaluated with two pathologists, diagnosing complicated partial mastectomy cases. The pathologists experienced that the prototype aided them during the review and that it created a better overall workflow. Conclusions: These results show that it is feasible to simplify the reporting tasks in a way that is not distracting, while at the same time being able to automatically extract the key findings. This simplification is possible due to the realization that the structured format needed for automatic extraction of data can be used to offload the pathologists' working memory during the diagnostic review.

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  • 115.
    Chen, Peng
    et al.
    Nanyang Technol Univ, Singapore.
    Liu, Xiaohu
    Nanyang Technol Univ, Singapore; Tsinghua Univ, Peoples R China.
    Goyal, Garima
    Nanyang Technol Univ, Singapore.
    Tran, Nhung Thi
    Nanyang Technol Univ, Singapore; Ho Chi Minh City Univ Technol and Educ, Vietnam.
    Ho, James Chin Shing
    Nanyang Technol Univ, Singapore.
    Wang, Yi
    Nanyang Technol Univ, Singapore; Wenzhou Med Univ, Peoples R China.
    Aili, Daniel
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Liedbereg, Bo
    Nanyang Technol Univ, Singapore; Nanyang Technol Univ, Singapore.
    Nanoplasmonic Sensing from the Human Vision Perspective2018In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 90, no 7, p. 4916-4924Article in journal (Refereed)
    Abstract [en]

    Localized surface plasmon resonance (LSPR) constitutes a versatile technique for biodetection, exploiting the sensitivity of plasmonic nanostructures to small changes in refractive index. The optical shift in the LSPR band caused by molecular interactions in the vicinity of the nanostructures are typically amp;lt;5 nm and can readily be detected by a spectrophotometer. Widespread use of LSPR-based sensors require cost-effective devices and would benefit from sensing schemes that enables use of very simple spectrophotometers or even naked-eye detection. This paper describes a new strategy facilitating visualization of minute optical responses in nanoplasmonic bioassays by taking into account the physiology of human color vision. We demonstrate, using a set of nine different plasmonic nanoparticles, that the cyan to green transition zone at similar to 500 nm is optimal for naked-eye detection of color changes. In this wavelength range, it is possible to detect a color change corresponding to a wavelength shift of similar to 2-3 nm induced by refractive index changes in the medium or by molecular binding to the surface of the nanoparticles. This strategy also can be utilized to improve the performance of aggregation-based nanoplasmonic colorimetric assays, which enables semiquantitative naked-eye detection of matrix metalloproteinase 7 (MMP7) activity at concentrations that are at least 5 times lower than previously reported assays using spherical gold nanoparticles. We foresee significant potential of this strategy in medical diagnostic and environmental monitoring, especially in situations where basic laboratory infrastructure is sparse or even nonexistent. Finally, we demonstrate that the developed concept can be used in combination with cell phone technology and red-green-blue (RGB) analysis for sensitive and quantitative detection of MMP7.

  • 116.
    Chen, Rong
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Georgii-Hemming, Patrik
    Department of Oncology, Uppsala University, Sweden.
    Åhlfeldt, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Representing a chemotherapy guideline using openEHR and rules2009In: Medical Informatics in a United and Healthy Europe / [ed] Klaus-Peter Adlassnig, Bernd Blobel, John Mantas, Izet Masic, IOS Press, 2009, Vol. 150, p. 653-657Conference paper (Refereed)
    Abstract [en]

    Computerized guidelines can provide decision support and facilitate the use of clinical guidelines. Several computerized guideline representation models (GRMs) exist but the poor interoperability between the guideline systems and the Electronic Health Record (EHR) systems limits their clinical usefulness. In this study we analyzed the clinical use of a published lymphoma chemotherapy guideline. We found that existing GRMs have limitations that can make it difficult to meet the clinical requirements. We hypothesized that guidelines could be represented as data and logic using openEHR archetypes, templates and rules. The design was tested by implementing the lymphoma guideline. We conclude that using the openEHR models and rules to represent chemotherapy guidelines is feasible and confers several advantages both from a clinical and from an informatics perspective.

  • 117.
    Chew, Michelle
    et al.
    Departments of Anaesthesia and Intensive Care, Institute of Experimental Clinical Research, Skejby Sygehus, Aarhus University Hospital, Denmark.
    Brandberg, Joakim
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Bjarum, Steinar
    Department of Biomerical Engineering, Trondheim University, Norway.
    Baek-Jensen, Katrine
    Institute of Experimental Clinical Research, Skejby Sygehus, Aarhus University Hospital, Denmark.
    Sloth, Erik
    Departments of Anaesthesia and Intensive Care, Skejby Sygehus, Aarhus University Hospital, Denmark.
    Ask, Per
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Hasenkam, J. Michael
    Department of Cardiothoracic Surgery, Skejby Sygehus, Aarhus University Hospital, Denmark.
    Janerot Sjöberg, Birgitta
    Linköping University, Department of Medicine and Care, Clinical Physiology. Linköping University, Faculty of Health Sciences.
    Pediatric cardiac output measurement using surface integration of velocity vectors: an in vivo validation study2000In: Critical Care Medicine, ISSN 0090-3493, E-ISSN 1530-0293, Vol. 28, no 11, p. 3664-3671Article in journal (Refereed)
    Abstract [en]

    Objective: To test the accuracy and reproducibility of systemic cardiac output (CO) measurements using surface integration of velocity vectors (SIVV) in a pediatric animal model with hemodynamic instability and to compare SIVV with traditional pulsed-wave Doppler measurements.

    Design: Prospective, comparative study.

    Setting: Animal research laboratory at a university medical center.

    Subjects: Eight piglets weighing 10-15 kg.

    Interventions: Hemodynamic instability was induced by using inhalation of isoflurane and infusions of colloid and dobutamine.

    Measurements: SIVV CO was measured at the left ventricular outflow tract, the aortic valve, and ascending aorta. Transit time CO was used as the reference standard.

    Results: There was good agreement between SIVV and transit time CO. At high frame rates, the mean difference ± 2 sd between the two methods was 0.01 ± 0.27 L/min for measurements at the left ventricular outflow tract, 0.08 ± 0.26 L/min for the ascending aorta, and 0.06 ± 0.25 L/min for the aortic valve. At low frame rates, measurements were 0.06 ± 0.25, 0.19 ± 0.32, and 0.14 ± 0.30 L/min for the left ventricular outflow tract, ascending aorta, and aortic valve, respectively. There were no differences between the three sites at high frame rates. Agreement between pulsed-wave Doppler and transit time CO was poorer, with a mean difference ± 2 sd of 0.09 ± 0.93 L/min. Repeated SIVV measurements taken at a period of relative hemodynamic stability differed by a mean difference ±2 sd of 0.01 ± 0.22 L/min, with a coefficient of variation = 7.6%. Intraobserver coefficients of variation were 5.7%, 4.9%, and 4.1% at the left ventricular outflow tract, ascending aorta, and aortic valve, respectively. Interobserver variability was also small, with a coefficient of variation = 8.5%.

    Conclusions: SIVV is an accurate and reproducible flow measurement technique. It is a considerable improvement over currently used methods and is applicable to pediatric critical care.

  • 118.
    Chougar, Lydia
    et al.
    Juntendo Univ, Japan; Hop Cochin, France.
    Hagiwara, Akifumi
    Juntendo Univ, Japan; Univ Tokyo, Japan.
    Takano, Nao
    Juntendo Univ, Japan.
    Andica, Christina
    Juntendo Univ, Japan.
    Cohen-Adad, Julien
    Juntendo Univ, Japan; Polytech Montreal, Canada; Univ Montreal, Canada.
    Warntjes, Marcel Jan Bertus
    Linköping University, Department of Health, Medicine and Caring Sciences, Division of Diagnostics and Specialist Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Clinical Physiology in Linköping. Linköping University, Center for Medical Image Science and Visualization (CMIV). SyntheticMR AB, Linkoping, Sweden.
    Maekawa, Tomoko
    Juntendo Univ, Japan; Univ Tokyo, Japan.
    Hori, Masaaki
    Juntendo Univ, Japan.
    Koshino, Saori
    Juntendo Univ, Japan; Univ Tokyo, Japan.
    Nakazawa, Misaki
    Juntendo Univ, Japan.
    Abe, Osamu
    Univ Tokyo, Japan.
    Aoki, Shigeki
    Juntendo Univ, Japan.
    Signal Intensity within Cerebral Venous Sinuses on Synthetic MRI2020In: MAGNETIC RESONANCE IN MEDICAL SCIENCES, ISSN 1347-3182, Vol. 19, no 1, p. 56-63Article in journal (Refereed)
    Abstract [en]

    Purpose: Flowing blood sometimes appears bright on synthetic T-1-weighted images, which could be misdiagnosed as a thrombus. This study aimed to investigate the frequency of hyperintensity within cerebral venous sinuses on synthetic MR images and to evaluate the influence of increasing flow rates on signal intensity using a flow phantom. Materials and Methods: Imaging data, including synthetic and conventional MRI scans, from 22 patients were retrospectively analyzed. Signal intensities at eight locations of cerebral venous sinuses on synthetic images were graded using the following three-point scale: 0, "dark vessel"; 1, "hyperintensity within the walls"; and 2, "hyperintensity within the lumen:" A phantom with gadolinium solution inside a U-shaped tube was acquired without flow and then with increasing flow rates (60, 100, 200, 300, 400 ml/min). Results: Considering all sinus locations, the venous signal intensity on synthetic T-1-weighted images was graded as 2 in 79.8% of the patients. On synthetic T-2-weighted images, all sinuses were graded as 0. On fluid-attenuated inversion recovery (FLAIR) images, sinuses were almost always graded as 0 (99.4%). In the phantom study, the signal initially became brighter on synthetic T-1-weighted images as the flow rate increased. Above a certain flow rate, the signal started to decrease. Conclusion: High signal intensity within the cerebral venous sinuses is a frequent finding on synthetic T-1-weighted images. This corresponds to the hyperintensity noted at certain flow rates in the phantom experiment.

  • 119.
    Cibis, Merih
    et al.
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Bustamante, Mariana
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Eriksson, Jonatan
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Carlhäll, Carljohan
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Clinical Physiology in Linköping. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Ebbers, Tino
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Clinical Physiology in Linköping. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Creating Hemodynamic Atlases of Cardiac 4D Flow MRI2017In: Journal of Magnetic Resonance Imaging, ISSN 1053-1807, E-ISSN 1522-2586, Vol. 46, no 5, p. 1389-1399Article in journal (Refereed)
    Abstract [en]

    Purpose: Hemodynamic atlases can add to the pathophysiological understanding of cardiac diseases. This study proposes a method to create hemodynamic atlases using 4D Flow magnetic resonance imaging (MRI). The method is demonstrated for kinetic energy (KE) and helicity density (Hd). Materials and Methods: Thirteen healthy subjects underwent 4D Flow MRI at 3T. Phase-contrast magnetic resonance cardioangiographies (PC-MRCAs) and an average heart were created and segmented. The PC-MRCAs, KE, and Hd were nonrigidly registered to the average heart to create atlases. The method was compared with 1) rigid, 2) affine registration of the PC-MRCAs, and 3) affine registration of segmentations. The peak and mean KE and Hd before and after registration were calculated to evaluate interpolation error due to nonrigid registration. Results: The segmentations deformed using nonrigid registration overlapped (median: 92.3%) more than rigid (23.1%, P amp;lt; 0.001), and affine registration of PC-MRCAs (38.5%, P amp;lt; 0.001) and affine registration of segmentations (61.5%, P amp;lt; 0.001). The peak KE was 4.9 mJ using the proposed method and affine registration of segmentations (P50.91), 3.5 mJ using rigid registration (P amp;lt; 0.001), and 4.2 mJ using affine registration of the PC-MRCAs (P amp;lt; 0.001). The mean KE was 1.1 mJ using the proposed method, 0.8 mJ using rigid registration (P amp;lt; 0.001), 0.9 mJ using affine registration of the PC-MRCAs (P amp;lt; 0.001), and 1.0 mJ using affine registration of segmentations (P50.028). The interpolation error was 5.262.6% at mid-systole, 2.863.8% at early diastole for peak KE; 9.669.3% at mid-systole, 4.064.6% at early diastole, and 4.964.6% at late diastole for peak Hd. The mean KE and Hd were not affected by interpolation. Conclusion: Hemodynamic atlases can be obtained with minimal user interaction using nonrigid registration of 4D Flow MRI. Level of Evidence: 2 Technical Efficacy: Stage 1

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  • 120.
    Cirillo, Marco Domenico
    et al.
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Mirdell, Robin
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Hand and Plastic Surgery.
    Sjöberg, Folke
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Hand and Plastic Surgery.
    Pham, Tuan
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Tensor Decomposition for Colour Image Segmentation of Burn Wounds2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 3291Article in journal (Refereed)
    Abstract [en]

    Research in burns has been a continuing demand over the past few decades, and important advancements are still needed to facilitate more effective patient stabilization and reduce mortality rate. Burn wound assessment, which is an important task for surgical management, largely depends on the accuracy of burn area and burn depth estimates. Automated quantification of these burn parameters plays an essential role for reducing these estimate errors conventionally carried out by clinicians. The task for automated burn area calculation is known as image segmentation. In this paper, a new segmentation method for burn wound images is proposed. The proposed methods utilizes a method of tensor decomposition of colour images, based on which effective texture features can be extracted for classification. Experimental results showed that the proposed method outperforms other methods not only in terms of segmentation accuracy but also computational speed.

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  • 121.
    Cirillo, Marco Domenico
    et al.
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Mirdell, Robin
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Hand and Plastic Surgery.
    Sjöberg, Folke
    Linköping University, Department of Clinical and Experimental Medicine, Division of Surgery, Orthopedics and Oncology. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Anaesthetics, Operations and Specialty Surgery Center, Department of Hand and Plastic Surgery.
    Pham, Tuan
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Time-Independent Prediction of Burn Depth using Deep Convolutional Neural Networks2019In: Journal of Burn Care & Research, ISSN 1559-047X, E-ISSN 1559-0488, Vol. 40, no 6, p. 857-863Article in journal (Refereed)
    Abstract [en]

    We present in this paper the application of deep convolutional neural networks, which are a state-of-the-art artificial intelligence (AI) approach in machine learning, for automated time-independent prediction of burn depth. Colour images of four types of burn depth injured in first few days, including normal skin and background, acquired by a TiVi camera were trained and tested with four pre-trained deep convolutional neural networks: VGG-16, GoogleNet, ResNet-50, and ResNet-101. In the end, the best 10-fold cross-validation results obtained from ResNet- 101 with an average, minimum, and maximum accuracy are 81.66%, 72.06% and 88.06%, respectively; and the average accuracy, sensitivity and specificity for the four different types of burn depth are 90.54%, 74.35% and 94.25%, respectively. The accuracy was compared to the clinical diagnosis obtained after the wound had healed. Hence, application of AI is very promising for prediction of burn depth and therefore can be a useful tool to help in guiding clinical decision and initial treatment of burn wounds.

    The full text will be freely available from 2020-06-11 08:35
  • 122.
    Claesson, Fredrik
    et al.
    Flodafors Lego AB.
    Andersson, Roger
    Katrineholms kommun.
    Hult, Peter
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, Faculty of Science & Engineering.
    CeMIDCARE - Kunskapscentrum för medicinsk teknik och innovationer inom distribuerad närvård.2006Conference paper (Other academic)
  • 123.
    Colantonio, Sara
    et al.
    CNR, Italy.
    Germanese, Danila
    CNR, Italy.
    Moroni, Davide
    CNR, Italy.
    Giorgi, Daniela
    CNR, Italy.
    Pascali, Mariantonietta
    CNR, Italy.
    Righi, Marco
    CNR, Italy.
    Coppini, Giuseppe
    CNR, Italy.
    Aurora Morales, Maria
    CNR, Italy.
    Chiarugi, Franco
    FORTH, Greece.
    Pediaditis, Mattew
    FORTH, Greece.
    Larsson, Marcus
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, Faculty of Science & Engineering.
    Strömberg, Tomas
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, Faculty of Science & Engineering.
    Henriquez, Pedro
    University of Central Lancashire, England.
    Matuszewski, Bogdan
    University of Central Lancashire, England.
    Milanic, Matijia
    Norwegian University of Science and Technology, Norway.
    Randeberg, Lise
    Norwegian University of Science and Technology, Norway.
    SEMEOTICONS - READING THE FACE CODE OF CARDIO-METABOLIC RISK2015In: 2015 INTERNATIONAL WORKSHOP ON COMPUTATIONAL INTELLIGENCE FOR MULTIMEDIA UNDERSTANDING (IWCIM), IEEE , 2015Conference paper (Refereed)
    Abstract [en]

    What if you could discover your health status by looking at yourself in the mirror? Since November 2013, the EU FP7 Project SEMEOTICONS is working to make this possible. The Project is building a multi-sensory device, having the form of a conventional mirror, able to read the semeiotic code of the face and detect possible evidence of the onset of cardio-metabolic diseases. The device, called Wize Mirror, integrates unobtrusive imaging sensors used to capture videos, images and 3D scans of the face. These are processed to assess the risk of a cardio-metabolic disease and thereby suggest possible strategies to prevent its onset.

  • 124.
    Cornet, Ronald
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Dentler, Kathrin
    Dept. of Computer Science, VU University Amsterdam, The Netherlands and Dept. of Medical Informatics, Academic Medical Center, University of Amsterdam, The Netherlands.
    Redundant Elements in SNOMED CT Concept Definitions2013In: proceedings of AIME 2013, Lecture Notes in ComputerScience 2013, Vol. 7885 / [ed] Peek, Niels, Marín Morales, Roque Luis, Peleg, Mor, Springer , 2013, p. 186-195Conference paper (Refereed)
    Abstract [en]

    While redundant elements in SNOMED CT concept definitions are harmless from a logical point of view, they unnecessarily make concept definitions of typically large ontologies such as SNOMED CT hard to construct and to maintain. In this paper, we apply a fully automated method to detect intra-axiom redundancies in SNOMED CT. We systematically analyse the completeness and soundness of the results of our method by examining the identified redundant elements. In absence of a gold standard, we check whether our method identifies concepts that are likely to contain redundant elements because they become equivalent to their stated subsumer when they are replaced by a fully defined concept with the same definition. To evaluate soundness, we remove all identified redundancies, and test whether the logical closure is preserved by comparing the concept hierarchy to the one of the official SNOMED CT distribution. We found that 35,010 of the 296,433 SNOMED CT concepts (12%) contain redundant elements in their definitions, and that the results of our method are sound and complete with respect to our partial evaluation. We recommend to free the stated form from these redundancies. In future, knowledge modellers should be supported by being pointed to newly introduced redundancies.

  • 125.
    Cornet, Ronald
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. University of Amsterdam, The Netherlands.
    Nyström, Mikael
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Karlsson, Daniel
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    User-Directed Coordination in SNOMED CT2013In: MedInfo 2013: Proceedings of the 14th World Congress on Medical and Health Informatics / [ed] Lehmann, C.U., Ammenwerth, E., Nøhr, C., Amsterdam: IOS Press, 2013, p. 72-76Conference paper (Refereed)
    Abstract [en]

    The possibility of post-coordination of SNOMED CT concepts, especially by clinical users, is both an asset and a challenge for SNOMED CT implementation. To get insight in the applicability of post-coordination, we analyzed scenarios for user-directed coordination that are described in the documentation of SNOMED CT. The analyses were based on experiences from previous and ongoing research and implementation work, including national mapping projects, and investigations on collection of data for multiple uses. These scenarios show various usability and representation problems: high number of relationships for refinement and qualification, improper options for refinement, incorrect formal definitions, and lack of support for applying editorial rules. Improved user-directed coordination in SNOMED CT in real practice requires advanced sanctioning, increased consistency of definitions of concepts in SNOMED CT, and real-time analysis of the post-coordinate expression.

  • 126.
    Cros, Olivier
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Borga, Magnus
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Pauwels, Elin
    University of Ghent, Belgium.
    Dirckx, Joris J. J.
    University of Antwerp, Belgium.
    Gaihede, Michael
    Aalborg University Hospital, Denmark.
    Micro-channels in the mastoid anatomy. Indications of a separate blood supply of the air cell system mucosa by micro-CT scanning2013In: Hearing Research, ISSN 0378-5955, E-ISSN 1878-5891, Vol. 301, p. 60-65Article in journal (Refereed)
    Abstract [en]

    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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  • 127.
    Cros, Olivier
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). Aalborg Unversity Hospital, Denmark.
    Eklund, Anders
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.
    Gaihede, Michael
    Department of Otolaryngology, Head & Neck Surgery, Aalborg University Hospital, Denmark.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Enhancement of micro-channels within the human mastoid bone based on local structure tensor analysis2016In: Image Proceessing Theory, Tools and Apllications, IEEE, 2016Conference paper (Refereed)
    Abstract [en]

    Numerous micro-channels have recently been discovered in the human temporal bone by x-ray micro-CT-scanning. After a preliminary study suggesting that these micro-channels form a separate blood supply for the mucosa of the mastoid air cells, a structural analysis of the micro-channels using a local structure tensor was carried out. Despite the high-resolution of the micro-CT scan, presence of noise within the air cells along with missing information in some micro-channels suggested the need of image enhancement. This paper proposes an adaptive enhancement of the micro-channels based on a local structure analysis while minimizing the impact of noise on the overall data. Comparison with an anisotropic diffusion PDE based scheme was also performed.

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  • 128.
    Cros, Olivier
    et al.
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). Department of Otolaryngology, Head & Neck Surgery, Aalborg University Hospital, Denmark.
    Gaihede, Michael
    Department of Otolaryngology, Head & Neck Surgery, Aalborg University Hospital, Denmark; Department of Clinical Medicine, Aalborg University, Denmark.
    Eklund, Anders
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Surface and curve skeleton from a structure tensor analysis applied on mastoid air cells in human temporal bones2017In: IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 2017, Institute of Electrical and Electronics Engineers (IEEE), 2017, p. 270-274Conference paper (Refereed)
    Abstract [en]

    The mastoid of human temporal bone contains numerous air cells connected to each others. In order to gain further knowledge about these air cells, a more compact representation is needed to obtain an estimate of the size distribution of these cells. Already existing skeletonization methods often fail in producing a faithful skeleton mostly due to noise hampering the binary representation of the data. This paper proposes a different approach by extracting geometrical information embedded in the Euclidean distance transform of a volume via a structure tensor analysis based on quadrature filters, from which a secondary structure tensor allows the extraction of surface skeleton along with a curve skeleton from its eigenvalues. Preliminary results obtained on a X-ray micro-CT scans of a human temporal bone show very promising results.

  • 129.
    Cros, Olivier
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV). Department of Otolaryngology, Head and Neck Surgery, Aalborg Hospital, Aarhus University Hospital, Denmark.
    Gaihede, Michael L.
    Department of Otolaryngology, Head and Neck Surgery, Aalborg Hospital, Aarhus University Hospital, Denmark.
    Borga, Magnus
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Smedby, Örjan
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Radiology. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Center for Diagnostics, Department of Radiology in Linköping.
    Mastoid structural properties determined by imaging analysis of high resolution CT-scanning2010In: Hearing Research, ISSN 0378-5955, E-ISSN 1878-5891, Vol. 263, no 1-2, p. 242-243Article in journal (Refereed)
    Abstract [en]

    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.

  • 130.
    Cubo, Ruben
    et al.
    Uppsala University, Sweden.
    Åström, Mattias
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, Faculty of Science & Engineering. Medtron Eindhoven Design Centre, Netherlands.
    Medvedev, Alexander
    Uppsala University, Sweden.
    Electric Field Modeling and Spatial Control in Deep Brain Stimulation2015In: 2015 54TH IEEE CONFERENCE ON DECISION AND CONTROL (CDC), IEEE , 2015, p. 3846-3851Conference paper (Refereed)
    Abstract [en]

    Deep Brain Stimulation (DBS) is an established treatment, in e.g. Parkinsons Disease, whose underlying biological mechanisms are unknown. In DBS, electrical stimulation is delivered through electrodes surgically implanted into certain regions of the brain of the patient. Mathematical models aiming at a better understanding of DBS and optimization of its therapeutical effect through the simulation of the electrical field propagating in the brain tissue have been developed in the past decade. The contribution of the present study is twofold: First, an analytical approximation of the electric field produced by an emitting contact is suggested and compared to the numerical solution given by a Finite Element Method (FEM) solver. Second, the optimal stimulation settings are evaluated by fitting the field distribution to a target one to control the spread of the stimulation. Optimization results are compared to those of a geometric approach, maximizing the intersection between the target and the activated volume in the brain tissue and reducing the stimulated area beyond said target. Both methods exhibit similar performance with respect to the optimal stimuli, with the electric field control approach being faster and more versatile.

  • 131.
    Dahlqvist Leinhard, Olof
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Radiation Physics.
    Linge, Jennifer
    Advanced MR Analytics AB, Linköping, Sweden.
    West, Janne
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Bell, Jimmy
    Westminster University, London, UK.
    Borga, Magnus
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering.
    Body Composition Profiling using MRI - Normative Data for Subjects with Cardiovascular Disease Extracted from the UK Biobank Imaging Cohort2016Conference paper (Other academic)
    Abstract [en]

    PURPOSE

    To describe the distribution of MRI-derived body composition measurements in subjects with cardiovascular disease (CVD) compared to subjects without any history of CVD.

    METHOD AND MATERIALS

    1864 males and 2036 females with an age range from 45 to 78 years from the UK Biobank imaging study were included in the study. Visceral adipose tissue volume normalized with height2 (VATi), total abdominal adipose tissue volume normalized with height2 (ATATi), total lean thigh muscle volume normalized with body weight (muscle ratio) and liver proton density fat fraction (PDFF) were measured with a 2-point Dixon imaging protocol covering neck to knee and a 10-point Dixon single slice protocol positioned within the liver using a 1.5T MR-scanner (Siemens, Germany). The MR-images were analyzed using AMRA® Profiler research (AMRA, Sweden). 213 subjects with history of cardiovascular events (angina, heart attack, or stroke) (event group) were age and gender matched to subjects with high blood pressure (HBP group), and subjects without CVD (controls).Kruskal-Wallis and Mann-Whitney U tests were used to test the observed differences for each measurement and group without correction for multiple comparisons.

    RESULTS

    VATi in the event group was 1.73 (1.13 - 2.32) l/m2 (median, 25%-75% percentile) compared to 1.68 (1.19 - 2.23) in the HBP group, and 1.30 (0.82-1.87) in the controls. ATATi in the event group was 4.31 (2.90-5.39) l/m2 compared to 4.05 (3.07-5.12) in the HBP group, and 3.48 (2.48-4.61) in the controls. Muscle ratio in the event group was 0.13 (0.12 - 0.15) l/kg as well as in the HBP group, compared to 0.14 (0.12 - 0.15) in the controls. Liver PDFF in the event group was 2.88 (1.77 - 7.72) % compared to 3.44 (2.04-6.18) in the HBP group, and 2.50 (1.58 - 5.15) in the controls. Kruskal-Wallis test showed significant differences for all variables and group comparisons (p<0.007). The post hoc test showed significant differences comparing the controls to both the event group and the HBP group. These were more significant for VATi and ATATi (p<10-4) than for muscle ratio and PDFF (p<0.03). No significant differences were detected between the event group and the HBP group.

    CONCLUSION

    Cardiovascular disease is strongly associated with high VATi, liver fat, and ATATi, and with low muscle ratio.

    CLINICAL RELEVANCE/APPLICATION

    The metabolic syndrome component in CVD can be effectively described using MRI-based body composition profiling.

  • 132.
    Dahlqvist Leinhard, Olof
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Radiation Physics.
    Linge, Jennifer
    Advanced MR Analytics AB, Linköping, Sweden.
    West, Janne
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Bell, Jimmy
    Westminster University, London, UK.
    Borga, Magnus
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Body Composition Profiling using MRI - Normative Data for Subjects with Diabetes Extracted from the UK Biobank Imaging Cohort2016Conference paper (Other academic)
    Abstract [en]

    PURPOSE

    To describe the distribution of MRI derived body composition measurements in subjects with diabetes mellitus (DM) compared to subjects without diabetes.

    METHOD AND MATERIALS

    3900 subjects (1864 males and 2036 females) from the UK Biobank imaging study were included in the study. The age range was 45 to 78 years. Visceral adipose tissue volume normalized with height2 (VATi), total abdominal adipose tissue volume normalized with height2 (ATATi), total lean thigh muscle volume normalized with body weight (muscle ratio) and liver proton density fat fraction (PDFF) were measured with a 6 minutes 2-point Dixon imaging protocol covering neck to knee and a 10-point Dixon single axial slice protocol positioned within the liver using a 1.5T MR-scanner (Siemens, Germany). The MR-images were analyzed using AMRA® Profiler research (AMRA, Sweden). 194 subjects with clinically diagnosed DM (DM group) were age and gender matched to subjects without DM (control group). For each variable and group, the median, 25%-percentile and 75%-percentile was calculated. Mann-Whitney U test was used to test the observed differences.

    RESULTS

    VATi in the DM group was 2.13 (1.43-2.62) l/m2 (median, 25% - 75% percentile) compared to 1.32 (0.86 - 1.79) l/m2 in the control group. ATATi in the DM group was 4.94 (3.86-6.19) l/m2 compared to 3.40 (2.56 - 4.70) l/m2 in the control group. Muscle ratio in the DM group was 0.13 (0.11 - 0.14) l/kg compared to 0.14 (0.12 - 0.15) l/kg in the control group. Liver PDFF in the DM group was 7.23 (2.68 - 13.26) % compared to 2.49 (1.53 - 4.73) % in the control group. Mann-Whitney U test detected significant differences between the DM group and the control group for all variables (p<10-5).

    CONCLUSION

    DM is strongly associated with high visceral fat, liver fat, and total abdominal fat, and low muscle ratio.

    CLINICAL RELEVANCE/APPLICATION

    Body composition profiling shows high potential to provide direct biomarkers to improve characterization and early diagnosis of DM.

  • 133.
    Dahlqvist Leinhard, Olof
    et al.
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medical and Health Sciences, Radiation Physics. Linköping University, Faculty of Health Sciences.
    Romu, Thobias
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Karlsson, Anette
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Borga, Magnus
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    High resolution isotropic whole-­‐body symmetrically sampled two point Dixon acquisition imaging at 3T2012In: ISMRM workshop on Fat-­‐Water Separation: Insights, Applications & Progress in MRI, 2012Conference paper (Other academic)
  • 134.
    Dahlqvist Leinhard, Olof
    et al.
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medical and Health Sciences, Radiation Physics. Linköping University, Faculty of Health Sciences.
    Romu, Thobias
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Kihlberg, Johan
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medical and Health Sciences, Radiology. Linköping University, Faculty of Health Sciences.
    Gjellan, Solveig
    Linköping University, Department of Medical and Health Sciences, Internal Medicine. Linköping University, Faculty of Health Sciences.
    Zanjani, Sepehr
    Linköping University, Department of Medical and Health Sciences, Internal Medicine. Linköping University, Faculty of Health Sciences.
    Smedby, Örjan
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Medical and Health Sciences, Radiology. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Centre for Diagnostics, Department of Radiology in Linköping.
    Nyström, Fredrik
    Linköping University, Department of Medical and Health Sciences, Internal Medicine. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart and Medicine Centre, Department of Endocrinology.
    Borga, Magnus
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Validation of whole-­‐body adipose tissue quantification using air displacement plethysmometry2012In: ISMRM workshop on Fat-­‐Water Separation: Insights, Applications & Progress in MRI, 2012Conference paper (Other academic)
  • 135.
    Danbolt, Christina
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Neuroscience. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Center for Diagnostics, Department of Clinical Pathology and Clinical Genetics.
    Hult, Peter
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, Faculty of Arts and Sciences.
    Grahn, Lita Tibbling
    Ask, Per
    Linköping University, Department of Biomedical Engineering, Physiological Measurements. Linköping University, The Institute of Technology.
    Validation and characterization of the computerized laryngeal analyzer (CLA) technique.1999In: Dysphagia (New York. Print), ISSN 0179-051X, E-ISSN 1432-0460, Vol. 14, no 4, p. 191-195Article in journal (Refereed)
    Abstract [en]

    The aim of this study was to investigate the response characteristics of the Computerized Laryngeal Analyzer (CLA) and the validity of the noninvasive CLA method to detect swallowing-induced laryngeal elevation correctly. Two healthy adults and two experimental models were used in the study. The CLA technique identified all swallowing events but was unable to discriminate between swallowing and other movements of the tongue or the neck. The computer program produced a derivated response to a square wave signal. Stepwise bending increments of the sensor displayed a linear amplitude response. The degree of laryngeal elevation could not be estimated with the CLA technique, and it was not possible to draw any reliable conclusions from the recordings as to whether the larynx was moving upward or downward.

  • 136.
    Danielis, Alessandro
    et al.
    CNR, Italy.
    Giorgi, Daniela
    CNR, Italy.
    Larsson, Marcus
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, Faculty of Science & Engineering.
    Strömberg, Tomas
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, Faculty of Science & Engineering.
    Colantonio, Sara
    CNR, Italy.
    Salvetti, Ovidio
    CNR, Italy.
    Lip segmentation based on Lambertian shadings and morphological operators for hyper-spectral images2017In: Pattern Recognition, ISSN 0031-3203, E-ISSN 1873-5142, Vol. 63, p. 355-370Article in journal (Refereed)
    Abstract [en]

    Lip segmentation is a non-trivial task because the colour difference between the lip and the skin regions maybe not so noticeable sometimes. We propose an automatic lip segmentation technique for hyper-spectral images from an imaging prototype with medical applications. Contrarily to many other existing lip segmentation methods, we do not use colour space transformations to localise the lip area. As input image, we use for the first time a parametric blood concentration map computed by using narrow spectral bands. Our method mainly consists of three phases: (i) for each subject generate a subset of face images enhanced by different simulated Lambertian illuminations, then (ii) perform lip segmentation on each enhanced image by using constrained morphological operations, and finally (iii) extract features from Fourier-based modeled lip boundaries for selecting the lip candidate. Experiments for testing our approach are performed under controlled conditions on volunteers and on a public hyper-spectral dataset. Results show the effectiveness of the algorithm against low spectral range, moustache, and noise.

  • 137.
    Davidsson, Anette
    et al.
    Östergötlands Läns Landsting, Heart and Medicine Center, Department of Clinical Physiology in Linköping.
    Georgiopoulos, C
    Östergötlands Läns Landsting, Heart and Medicine Center, Department of Clinical Physiology in Linköping.
    Gustafsson, Agnetha
    Linköping University, Department of Medical and Health Sciences, Radiation Physics. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Center for Surgery, Orthopaedics and Cancer Treatment, Department of Radiation Physics.
    Zachrisson, Helene
    Östergötlands Läns Landsting, Heart and Medicine Center, Department of Clinical Physiology in Linköping.
    Evaluation and comparison of quantification tools for early diagnosis of Parkinson's disease with DaTSCAN SPECT.2011Conference paper (Refereed)
  • 138.
    Davidsson, Anette
    et al.
    Östergötlands Läns Landsting, Heart and Medicine Centre, Department of Clinical Physiology UHL.
    Georgiopoulos, C
    Östergötlands Läns Landsting, Heart and Medicine Centre, Department of Clinical Physiology UHL.
    Gustafsson, Agnetha
    Linköping University, Department of Medical and Health Sciences, Radiation Physics. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Centre for Surgery, Orthopaedics and Cancer Treatment, Department of Radiation Physics UHL.
    Zachrisson, Helene
    Östergötlands Läns Landsting, Heart and Medicine Centre, Department of Clinical Physiology UHL.
    Utvärdering och jämförelse av kvantifieringsverktyg för tidig diagnostik av Parkinsons sjukdom med DaTSCAN SPECT2011Conference paper (Other academic)
  • 139.
    De Biase, Alessia
    Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning.
    Generative Adversarial Networks to enhance decision support in digital pathology2019Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
    Abstract [en]

    Histopathological evaluation and Gleason grading on Hematoxylin and Eosin(H&E) stained specimens is the clinical standard in grading prostate cancer. Recently, deep learning models have been trained to assist pathologists in detecting prostate cancer. However, these predictions could be improved further regarding variations in morphology, staining and differences across scanners. An approach to tackle such problems is to employ conditional GANs for style transfer. A total of 52 prostatectomies from 48 patients were scanned with two different scanners. Data was split into 40 images for training and 12 images for testing and all images were divided into overlapping 256x256 patches. A segmentation model was trained using images from scanner A, and the model was tested on images from both scanner A and B. Next, GANs were trained to perform style transfer from scanner A to scanner B. The training was performed using unpaired training images and different types of Unsupervised Image to Image Translation GANs (CycleGAN and UNIT). Beside the common CycleGAN architecture, a modified version was also tested, adding Kullback Leibler (KL) divergence in the loss function. Then, the segmentation model was tested on the augmented images from scanner B.The models were evaluated on 2,000 randomly selected patches of 256x256 pixels from 10 prostatectomies. The resulting predictions were evaluated both qualitatively and quantitatively. All proposed methods outperformed in AUC, in the best case the improvement was of 16%. However, only CycleGAN trained on a large dataset demonstrated to be capable to improve the segmentation tool performance, preserving tissue morphology and obtaining higher results in all the evaluation measurements. All the models were analyzed and, finally, the significance of the difference between the segmentation model performance on style transferred images and on untransferred images was assessed, using statistical tests.

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    Master Thesis
  • 140.
    De Biase, Alessia
    et al.
    Division of Statistics and Machine learning, Department of Computer and Information Science, Linkoping University, Linkoping, Sweden, ContextVision AB, Stockholm, Sweden .
    Burlutskiy, Nikolay
    ContextVision AB, Stockholm, Sweden .
    Pinchaud, Nicolas
    ContextVision AB, Stockholm, Sweden.
    Eklund, Anders
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Deep Learning Data Augmentation Approach to Improve Cancer Segmentation Performance across Different Scanners2019Conference paper (Refereed)
  • 141. Order onlineBuy this publication >>
    De Geer, Jakob
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    On the use of computed tomography in cardiac imaging2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Background

    Cardiac Computed Tomography Angiography (CCTA) is becoming increasingly useful in the work‐up of coronary artery disease (CAD). Several potential methods for increasing the diagnostic yield of cardiac CT are available.

    Purpose

    Study I: To investigate whether the use of a 2‐D, non‐linear adaptive noise reduction filter can improve CCTA image quality.

    Study II: To evaluate the variation in adenosine stress dynamic CT perfusion (CTP) blood flow as compared to stress 99mTc SPECT. Secondly, to compare the perfusion results from manual and automatic myocardial CTP segmentation.

    Study III: To evaluate the accuracy of non‐invasive, CCTA‐derived Fractional Flow Reserve (cFFR).

    Study IV: To evaluate the prognostic value of CCTA in terms of major adverse cardiac events (MACE).

    Materials and methods

    Study I: Single images from 36 consecutive CCTA exams performed with two different dose levels were used. Image quality in full dose, low‐dose and noise‐reduced low‐dose images was graded using visual grading analysis. Image noise was measured.

    Study II: CTP and SPECT were performed in 17 patients, and the variation in per AHA‐segment blood flow was evaluated and compared. CTP results from manual and automated image segmentation were compared.

    Study III: CCTA datasets from 21 patients were processed using cFFR software and the results compared to the corresponding invasively measured FFR (invFFR).

    Study IV: 1205 consecutive patients with chest pain of unknown origin underwent CCTA. Baseline data and data on subsequent MACE were retrieved from relevant registries. Survival, hazard ratios and the three‐year incidence of cardiac events and readmissions were calculated.

    Results

    Study I: There was significant improvement in perceived image quality for all criteria when the filter was applied, and a significant decrease in image noise.

    Study II: The correlation coefficients for CTP vs. SPECT were 0.38 and 0.41 (p<0.001, for manual and automated segmentation respectively. Mean per patient CTP blood flow in normal segments varied between 94‐183 ml/100 ml tissue/min for manual segmentation, and 104‐196 ml/100 ml tissue/min for automated segmentation. The Spearman rank correlation coefficient for manual vs. automated segmentation CTP was ρ = 0.88 (p<0.001) and the Intraclass Correlation Coefficient (ICC) was 0.93 (p<0.001).

    Study III: The Spearman rank correlation coefficient for cFFR vs. invFFR was ρ = 0.77 (p<0.001) and the ICC was 0.73 (p<0.001). Sensitivity, specificity, positive predictive value and negative predictive value for significant stenosis (FFR<0.80, per vessel) were 0.83, 0.76, 0.56 and 0.93 respectively.

    Study IV: The hazard ratio for non‐obstructive CAD vs. normal coronary arteries was 5.13 (95% C.I 1.03‐25.43, p<0.05), and 151.40 (95% C.I 37.03‐619.08, p<0.001) for obstructive CAD vs. normal coronary arteries. The three‐year incidence of MACE was 1.1% for patients with normal vessels on CCTA, 2.5% for patients with non‐obstructive CAD and 42.7% for patients with obstructive CAD (p<0.001).

    Conclusions:

    Study I: Image quality and noise levels of low dose images were significantly improved with the filter, even though the improvement was small compared to the image quality of the corresponding diastolic full‐dose images.

    Study II: Correlation between dynamic CTP and SPECT was positive but weak. There were large variations in CTP blood flow in normal segments on SPECT, rendering the definition of an absolute cut‐off value for normal vs. ischemic myocardium difficult. Manual and automatic segmentation were equally useful.

    Study III: The correlation between cFFR and invFFR was good, indicating that noninvasively estimated cFFR performs on a similar level as invasively measure FFR.

    Study IV: The long‐term risk for MACE was very low in patients without obstructive CAD on CCTA, though there seemed to be a substantial increase in the risk for MACE even in patients with non‐obstructive CAD as compared to normal coronary arteries. In addition, even patients with normal coronary arteries or non‐obstructive CAD continued to have a substantial number of readmissions for chest pain or angina pectoris.

    List of papers
    1. The efficacy of 2D, non-linear noise reduction filtering in cardiac imaging: a pilot study
    Open this publication in new window or tab >>The efficacy of 2D, non-linear noise reduction filtering in cardiac imaging: a pilot study
    2011 (English)In: Acta Radiologica, ISSN 0284-1851, E-ISSN 1600-0455, Vol. 52, no 7, p. 716-722Article in journal (Refereed) Published
    Abstract [en]

    Background: Computed tomography (CT) is becoming increasingly popular as a non-invasive method for visualizing the coronary arteries but patient radiation doses are still an issue. Postprocessing filters such as 2D adaptive non-linear filters might help to reduce the dose without loss of image quality. less thanbrgreater than less thanbrgreater thanPurpose: To investigate whether the use of a 2D, non-linear adaptive noise reduction filter can improve image quality in cardiac computed tomography angiography (CCTA). less thanbrgreater than less thanbrgreater thanMaterial and Methods: CCTA examinations were performed in 36 clinical patients on a dual source CT using two patient dose levels: maximum dose during diastole and reduced dose (20% of maximum dose) during systole. One full-dose and one reduced-dose image were selected from each of the examinations. The reduced-dose image was duplicated and one copy postprocessed using a 2D non-linear adaptive noise reduction filter, resulting in three images per patient. Image quality was assessed using visual grading with three criteria from the European guidelines for assessment of image quality and two additional criteria regarding the left main artery and the overall image quality. Also, the HU value and its standard deviation were measured in the ascending and descending aorta. Data were analyzed using Visual Grading Regression and paired t-test. less thanbrgreater than less thanbrgreater thanResult: For all five criteria, there was a significant (P andlt; 0.01 or better) improvement in perceived image quality when comparing postprocessed low-dose images with low-dose images without noise reduction. Comparing full dose images with postprocessed low-dose images resulted in a considerably larger, significant (P andlt; 0.001) difference. Also, there was a significant reduction of the standard deviation of the HU values in the ascending and descending aorta when comparing postprocessed low-dose images with low-dose images without postprocessing. less thanbrgreater than less thanbrgreater thanConclusion: Even with an 80% dose reduction, there was a significant improvement in the perceived image quality when using a 2D noise-reduction filter, though not approaching the quality of full-dose images. This indicates that cardiac CT examinations could benefit from noise-reducing postprocessing with 2D non-linear adaptive filters.

    Place, publisher, year, edition, pages
    Informa Healthcare / Wiley-Blackwell / Royal Society of Medicine Press, 2011
    Keywords
    Cardiac, CT angiography, heart, adults, image manipulation
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-71803 (URN)10.1258/ar.2011.100511 (DOI)000295759600007 ()
    Available from: 2011-11-04 Created: 2011-11-04 Last updated: 2017-12-08
    2. Large variation in blood flow between left ventricular segments, as detected by adenosine stress dynamic CT perfusion.
    Open this publication in new window or tab >>Large variation in blood flow between left ventricular segments, as detected by adenosine stress dynamic CT perfusion.
    Show others...
    2015 (English)In: Clinical Physiology and Functional Imaging, ISSN 1475-0961, E-ISSN 1475-097X, Vol. 35, no 4, p. 291-300Article in journal (Refereed) Published
    Abstract [en]

    BACKGROUND: Dynamic cardiac CT perfusion (CTP) is based on repeated imaging during the first-pass contrast agent inflow. It is a relatively new method that still needs validation.

    PURPOSE: To evaluate the variation in adenosine stress dynamic CTP blood flow as compared to (99m) Tc SPECT. Secondarily, to compare manual and automatic segmentation.

    METHODS: Seventeen patients with manifest coronary artery disease were included. Nine were excluded from evaluation for various reasons. All patients were examined with dynamic stress CTP and stress/rest SPECT. CTP blood flow was compared with SPECT on a per segment basis. Results for manual and automated AHA segmentation were compared.

    RESULTS: CTP showed a positive correlation with SPECT, with correlation coefficients of 0·38 and 0·41 for manual and automatic segmentation, respectively (P<0·0001). There was no significant difference between the correlation coefficients of the manual and automated segmentation procedures (P = 0·75). The average per individual global CTP blood flow value for normal segments varied by a factor of 1·9 (manual and automatic segmentation). For the whole patient group, the CTP blood flow value in normal segments varied by a factor of 2·9/2·7 (manual/automatic segmentation). Within each patient, the average per segment blood flow in normal segments varied by a factor of 1·3-2·0/1·2-2·1 (manual/automatic segmentation).

    CONCLUSION: A positive but rather weak correlation was found between CTP and (99m) Tc SPECT. Large variations in CTP blood flow suggest that a cut-off value for stress myocardial blood flow is inadequate to detect ischaemic segments. Dynamic CTP is hampered by a limited coverage.

    National Category
    Clinical Medicine
    Identifiers
    urn:nbn:se:liu:diva-113400 (URN)10.1111/cpf.12163 (DOI)000356312800007 ()24842265 (PubMedID)
    Available from: 2015-01-17 Created: 2015-01-17 Last updated: 2017-12-05
    3. Software-based on-site estimation of fractional flow reserve using standard coronary CT angiography data.
    Open this publication in new window or tab >>Software-based on-site estimation of fractional flow reserve using standard coronary CT angiography data.
    Show others...
    2016 (English)In: Acta Radiologica, ISSN 0284-1851, E-ISSN 1600-0455, Vol. 57, no 10, p. 1186-1192Article in journal (Refereed) Published
    Abstract [en]

    BACKGROUND: The significance of a coronary stenosis can be determined by measuring the fractional flow reserve (FFR) during invasive coronary angiography. Recently, methods have been developed which claim to be able to estimate FFR using image data from standard coronary computed tomography angiography (CCTA) exams.

    PURPOSE: To evaluate the accuracy of non-invasively computed fractional flow reserve (cFFR) from CCTA.

    MATERIAL AND METHODS: A total of 23 vessels in 21 patients who had undergone both CCTA and invasive angiography with FFR measurement were evaluated using a cFFR software prototype. The cFFR results were compared to the invasively obtained FFR values. Correlation was calculated using Spearman's rank correlation, and agreement using intraclass correlation coefficient (ICC). Sensitivity, specificity, accuracy, negative predictive value, and positive predictive value for significant stenosis (defined as both FFR ≤0.80 and FFR ≤0.75) were calculated.

    RESULTS: The mean cFFR value for the whole group was 0.81 and the corresponding mean invFFR value was 0.84. The cFFR sensitivity for significant stenosis (FFR ≤0.80/0.75) on a per-lesion basis was 0.83/0.80, specificity was 0.76/0.89, and accuracy 0.78/0.87. The positive predictive value was 0.56/0.67 and the negative predictive value was 0.93/0.94. The Spearman rank correlation coefficient was ρ = 0.77 (P < 0.001) and ICC = 0.73 (P < 0.001).

    CONCLUSION: This particular CCTA-based cFFR software prototype allows for a rapid, non-invasive on-site evaluation of cFFR. The results are encouraging and cFFR may in the future be of help in the triage to invasive coronary angiography.

    Place, publisher, year, edition, pages
    Sage Publications, 2016
    Keywords
    Cardiac; computed tomography angiography (CTA); heart; arteries; adults; computer applications – detection/diagnosis
    National Category
    Radiology, Nuclear Medicine and Medical Imaging
    Identifiers
    urn:nbn:se:liu:diva-123579 (URN)10.1177/0284185115622075 (DOI)000382967500007 ()26691914 (PubMedID)
    Note

    Funding agencies: Department of Radiology, Region Ostergotland; Swedish Heart-Lung-foundation [20120449]

    Available from: 2015-12-29 Created: 2015-12-29 Last updated: 2017-12-01Bibliographically approved
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  • 142.
    Dela Haije, Tom
    et al.
    Univ Copenhagen, Denmark.
    Özarslan, Evren
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Feragen, Aasa
    Tech Univ Denmark, Denmark.
    Enforcing necessary non-negativity constraints for common diffusion MRI models using sum of squares programming2020In: NeuroImage, ISSN 1053-8119, E-ISSN 1095-9572, Vol. 209, article id 116405Article in journal (Refereed)
    Abstract [en]

    In this work we investigate the use of sum of squares constraints for various diffusion-weighted MRI models, with a goal of enforcing strict, global non-negativity of the diffusion propagator. We formulate such constraints for the mean apparent propagator model and for spherical deconvolution, guaranteeing strict non-negativity of the corresponding diffusion propagators. For the cumulant expansion similar constraints cannot exist, and we instead derive a set of auxiliary constraints that are necessary but not sufficient to guarantee non-negativity. These constraints can all be verified and enforced at reasonable computational costs using semidefinite programming. By verifying our constraints on standard reconstructions of the different models, we show that currently used weak constraints are largely ineffective at ensuring non-negativity. We further show that if strict non-negativity is not enforced then estimated model parameters may suffer from significant errors, leading to serious inaccuracies in important derived quantities such as the main fiber orientations, mean kurtosis, etc. Finally, our experiments confirm that the observed constraint violations are mostly due to measurement noise, which is difficult to mitigate and suggests that properly constrained optimization should currently be considered the norm in many cases.

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    fulltext
  • 143.
    Dembek, Till A.
    et al.
    Department of Neurology, University of Cologne, Cologne, Germany; Department of Stereotaxy and Functional Neurosurgery, University of Cologne, Cologne, Germany.
    Barbe, Michael T
    Department of Neurology, University of Cologne, Cologne, Germany.
    Åström, Mattias
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, Faculty of Science & Engineering. Medtronic Neuromodulation, Medtronic Eindhoven Design Center, Eindhoven, The Netherlands.
    Hoevels, Mauritius
    Department of Stereotaxy and Functional Neurosurgery, University of Cologne, Cologne, Germany.
    Visser-Vandewalle, Veerle
    Department of Stereotaxy and Functional Neurosurgery, University of Cologne, Cologne, Germany.
    Fink, Gereon R
    Department of Neurology, University of Cologne, Cologne, Germany.
    Timmermann, Lars
    Department of Neurology, University of Cologne, Cologne, Germany.
    Probabilistic mapping of deep brain stimulation effects in essential tremor2017In: NeuroImage: Clinical, ISSN 0353-8842, E-ISSN 2213-1582, Vol. 13Article in journal (Refereed)
    Abstract [en]

    Objective

    To create probabilistic stimulation maps (PSMs) of deep brain stimulation (DBS) effects on tremor suppression and stimulation-induced side-effects in patients with essential tremor (ET).

    Method

    Monopolar reviews from 16 ET-patients which consisted of over 600 stimulation settings were used to create PSMs. A spherical model of the volume of neural activation was used to estimate the spatial extent of DBS for each setting. All data was pooled and voxel-wise statistical analysis as well as nonparametric permutation testing was used to confirm the validity of the PSMs.

    Results

    PSMs showed tremor suppression to be more pronounced by stimulation in the zona incerta (ZI) than in the ventral intermediate nucleus (VIM). Paresthesias and dizziness were most commonly associated with stimulation in the ZI and surrounding thalamic nuclei.

    Discussion

    Our results support the assumption, that the ZI might be a very effective target for tremor suppression. However stimulation inside the ZI and in its close vicinity was also related to the occurrence of stimulation-induced side-effects, so it remains unclear whether the VIM or the ZI is the overall better target. The study demonstrates the use of PSMs for target selection and evaluation. While their accuracy has to be carefully discussed, they can improve the understanding of DBS effects and can be of use for other DBS targets in the therapy of neurological or psychiatric disorders as well. Furthermore they provide a priori information about expected DBS effects in a certain region and might be helpful to clinicians in programming DBS devices in the future.

    Abbreviations: DBS, Deep brain stimulation; ET, Essential tremor; PSA, Posterior subthalamic area; PSM, Probabilistic stimulation map; VIM, Ventral intermediate nucleus; VNA, Volume of neural activation; ZI, Zona incerta

  • 144.
    Deniz, Daniel
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Causes of multimodality of efficiency gain distributions in accelerated Monte Carlo based dose calculations for brachytherapy planning using correlated sampling2009Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Fixed-collision correlated sampling for Monte Carlo (MC) simulations is a method which can be used in order to shorten the simulation time for brachytherapy treatment planning in a 3D patient geometry. The increased efficiency compared to conventional MC simulation is measured by efficiency gain. However, a previous study showed that, in some cases, PDFs (probability density functions) of estimates of the efficiency gain, simulated using resampling and other MC methods, were multimodal with values below 1. This means that the method was less effective than conventional sampling for these cases. The aims of this thesis were to trace the causes of the multimodal distributions and to propose techniques to mitigate the problem caused by photons with high statistical weights.Two simulation environments were used for the study case, a homogeneous and a heterogeneous environment. The homogenous environment consisted of a water sphere with the radius 100mm. For the heterogeneous environment a cylindrical block of tungsten alloy (diameter 15 mm, height 2.5 mm) was placed in the water sphere. The sphere was divided into an array of cubic voxels of size 2.5 mm x 2.5 mm x 2.5 mm for dose calculations. A photon source was positioned in the middle of the water sphere and emitted photons with the energy 400 keV.It was found that the low values and multimodal PDFs for the efficiency gain estimates originated from photons depositing high values of energy in some voxels in the heterogeneous environment. The high energy deposits were due to extremely high statistical weights of photons interacting repeatedly in the highly attenuating tungsten cylinder. When photon histories contributing to the rare events of high energy deposits (outliers) were removed, the PDFs became uni-modal and efficiency gain increased. However, removing outliers will cause results to be biased calling for other techniques to handle the problem with high statistical weights.One way to resolve the problem in the current implementation of the fixed-collision correlated sampling scheme in PTRAN (the MC code used) could be to split photons with high statistical weights into several photons with the same sum weight as the initial photon. The splitting of photons will result in more time consuming simulations in areas with high attenuation coefficients, which may not be the areas of interest. This could be resolved by using Russian roulette, eliminating some of the photons with high statistical weight in such areas.Fixed-collision correlated sampling for Monte Carlo (MC) simulations is a method which can be used in order to shorten the simulation time for brachytherapy treatment planning in a 3D patient geometry. The increased efficiency compared to conventional MC simulation is measured by efficiency gain. However, a previous study showed that, in some cases, PDFs (probability density functions) of estimates of the efficiency gain, simulated using resampling and other MC methods, were multimodal with values below 1. This means that the method was less effective than conventional sampling for these cases. The aims of this thesis were to trace the causes of the multimodal distributions and to propose techniques to mitigate the problem caused by photons with high statistical weights.Two simulation environments were used for the study case, a homogeneous and a heterogeneous environment. The homogenous environment consisted of a water sphere with the radius 100mm. For the heterogeneous environment a cylindrical block of tungsten alloy (diameter 15 mm, height 2.5 mm) was placed in the water sphere. The sphere was divided into an array of cubic voxels of size 2.5 mm x 2.5 mm x 2.5 mm for dose calculations. A photon source was positioned in the middle of the water sphere and emitted photons with the energy 400 keV.It was found that the low values and multimodal PDFs for the efficiency gain estimates originated from photons depositing high values of energy in some voxels in the heterogeneous environment. The high energy deposits were due to extremely high statistical weights of photons interacting repeatedly in the highly attenuating tungsten cylinder. When photon histories contributing to the rare events of high energy deposits (outliers) were removed, the PDFs became uni-modal and efficiency gain increased. However, removing outliers will cause results to be biased calling for other techniques to handle the problem with high statistical weights.One way to resolve the problem in the current implementation of the fixed-collision correlated sampling scheme in PTRAN (the MC code used) could be to split photons with high statistical weights into several photons with the same sum weight as the initial photon. The splitting of photons will result in more time consuming simulations in areas with high attenuation coefficients, which may not be the areas of interest. This could be resolved by using Russian roulette, eliminating some of the photons with high statistical weight in such areas.

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  • 145.
    Dentler, Kathrin
    et al.
    Dept. of Computer Science, VU University Amsterdam, The Netherlands and Dept. of Medical Informatics, Academic Medical Center, University of Amsterdam, The Netherlands.
    Ten Teije, Annette
    Dept. of Computer Science, VU University Amsterdam, The Netherlands.
    de Keizer, Nicolette
    Dept. of Medical Informatics, Academic Medical Center, University of Amsterdam, The Netherlands.
    Cornet, Ronald
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Barriers to the reuse of routinely recorded clinical data: a field report2013In: Proceedings of Studies in Health Technology & Informatics, vol.192, IOS Press, 2013, Vol. 192, p. 313-317Conference paper (Refereed)
    Abstract [en]

    Today, clinical data is routinely recorded in vast amounts, but its reuse can be challenging. A secondary use that should ideally be based on previously collected clinical data is the computation of clinical quality indicators. In the present study, we attempted to retrieve all data from our hospital that is required to compute a set of quality indicators in the domain of colorectal cancer surgery. We categorised the barriers that we encountered in the scope of this project according to an existing framework, and provide recommendations on how to prevent or surmount these barriers. Assuming that our case is not unique, these recommendations might be applicable for the design, evaluation and optimisation of Electronic Health Records.

  • 146.
    Deshpande, S.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics.
    Tiwari, A.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics.
    Turner, A.P.F.
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics.
    Smart auto-switchable cardiac troponin immunosensor for diagnosis of cardiac injury2012Conference paper (Refereed)
  • 147.
    Dickens, Erik
    Linköping University, Department of Science and Technology.
    Towards automatic detection and visualization of tissues in medical volume rendering2006Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The technique of volume rendering can be a powerful tool when visualizing 3D medical data sets. Its characteristic of capturing 3D internal structures within a 2D rendered image makes it attractive in the analysis. However, the applications that implement this technique fail to reach out to most of the supposed end-users at the clinics and radiology departments of today. This is primarily due to problems centered on the design of the Transfer Function (TF), the tool that makes tissues visually appear in the rendered image. The interaction with the TF is too complex for a supposed end-user and its capability of separating tissues is often insufficient. This thesis presents methods for detecting the regions in the image volume where tissues are contained. The tissues that are of interest can furthermore be identified among these regions. This processing and classification is possible thanks to the use of a priori knowledge, i.e. what is known about the data set and its domain in advance. The identified regions can finally be visualized using tissue adapted TFs that can create cleaner renderings of tissues where a normal TF would fail to separate them. In addition an intuitive user control is presented that allows the user to easily interact with the detection and the visualization.

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  • 148. Order onlineBuy this publication >>
    Diczfalusy, Elin
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Modeling and Simulation of Microdialysis in the Deep Brain Structures2012Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Microdialysis is a method for monitoring of the local biochemical environment in a region of interest. The method uses a catheter, mimicking the function of a blood capillary, to sample substances from the surrounding medium through diffusion. A recent application for microdialysis is the sampling of neuroactive substances in the deep brain, or basal ganglia, during deep brain stimulation (DBS) for patients with Parkinson’s disease. The basal ganglia consist of nuclei interconnected by chemical synapses, and it is hypothesized that the levels of neurotransmitter substances around the synapses are affected by DBS treatment. In order to relate the microdialysis data to their anatomical origin and to the effects of DBS, it is suitable to estimate the tissue volume which is sampled during a microdialysis experiment. In this thesis, the maximum tissue volume of influence (TVImax) for a microdialysis catheter was simulated and evaluated using the finite element method (FEM), to allow interpretation of biochemical data in relation to anatomical structures.

    A FEM model for simulation of the TVImax for a microdialysis catheter placed in grey brain matter was set up, using Fick’s law of diffusion. The model was used to investigate the impact of the analyte diffusion coefficient (D), the tissue tortuosity (λ) and the loss rate constant (k) on the size of the TVImax by regression analysis. Using relevant parameter intervals, the radius of the TVImax of a neurotransmitter was estimated to 0.85 ± 0.25 mm. A microdialysis experiment on calf brain tissue showed agreement with the regression model. A heterogeneous anisotropic FEM model based on diffusion tensor imaging (DTI) showed that the radius of the TVImax may vary by up to 0.5 mm as a consequence of local tissue properties, which was reasonable in relation to the 95% confidence interval from the regression estimation. The TVImax was simulated and patient-specifically visualized in relation to MRI images for four patients undergoing microdialysis in parallel to DBS. The size of the TVImax showed to be relevant in relation to the basal ganglia nuclei, and the obtained microdialysis data indicated that the biochemical response to DBS depends on the catheter position. The simulations of the TVImax were combined with patient-specific DBS electric field simulations, for further interpretation of the results in relation to the effects of DBS.

    In conclusion, simulations and visualizations of the TVImax allowed relating microdialysis data to its anatomical origin. Detailed knowledge about the parameters affecting the microdialysis sampling volume is valuable for the current application as well as other applications related to the migration of analytes in tissue.

    List of papers
    1. A model for simulation and patient-specific visualization of the tissue volume of influence during brain microdialysis
    Open this publication in new window or tab >>A model for simulation and patient-specific visualization of the tissue volume of influence during brain microdialysis
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    2011 (English)In: Medical and Biological Engineering and Computing, ISSN 0140-0118, E-ISSN 1741-0444, Vol. 49, no 12, p. 1459-1469Article in journal (Refereed) Published
    Abstract [en]

    Microdialysis can be used in parallel to deep brain stimulation (DBS) to relate biochemical changes to the clinical outcome. The aim of the study was to use the finite element method to predict the tissue volume of influence (TVI(max)) and its cross-sectional radius (r (TVImax)) when using brain microdialysis, and visualize the TVI(max) in relation to patient anatomy. An equation based on Fick's law was used to simulate the TVI(max). Factorial design and regression analysis were used to investigate the impact of the diffusion coefficient, tortuosity and loss rate on the r (TVImax). A calf brain tissue experiment was performed to further evaluate these parameters. The model was implemented with pre-(MRI) and post-(CT) operative patient images for simulation of the TVI(max) for four patients undergoing microdialysis in parallel to DBS. Using physiologically relevant parameter values, the r (TVImax) for analytes with a diffusion coefficient D = 7.5 × 10(-6) cm(2)/s was estimated to 0.85 ± 0.25 mm. The simulations showed agreement with experimental data. Due to an implanted gold thread, the catheter positions were visible in the post-operative images. The TVI(max) was visualized for each catheter. The biochemical changes could thereby be related to their anatomical origin, facilitating interpretation of results.

    Place, publisher, year, edition, pages
    Springer Publishing Company, 2011
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-72911 (URN)10.1007/s11517-011-0841-0 (DOI)000297550600012 ()22081236 (PubMedID)
    Available from: 2011-12-09 Created: 2011-12-09 Last updated: 2018-01-12Bibliographically approved
    2. Simulations and visualizations for interpretation of brain microdialysis data during deep brain stimulation
    Open this publication in new window or tab >>Simulations and visualizations for interpretation of brain microdialysis data during deep brain stimulation
    Show others...
    2012 (English)In: IEEE Engineering in Medicine and Biology Society (EMBC), 2012, IEEE , 2012, p. 6438-6441Conference paper, Published paper (Refereed)
    Abstract [en]

    Microdialysis of the basal ganglia was used in parallel to deep brain stimulation (DBS) for patients with Parkinson’s disease. The aim of this study was to patientspecifically simulate and visualize the maximum tissue volume of influence (TVImax) for each microdialysis catheter and the electric field generated around each DBS electrode. The finite element method (FEM) was used for the simulations. The method allowed mapping of the anatomical origin of the microdialysis data and the electric stimulation for each patient. It  was seen that the sampling and stimulation targets differed among the patients, and the results will therefore be used in the future interpretation of the biochemical data.

    Place, publisher, year, edition, pages
    IEEE, 2012
    Series
    IEEE Engineering in Medicine and Biology Society Conference Proceedings, ISSN 1557-170X
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-84275 (URN)10.1109/EMBC.2012.6347468 (DOI)000313296506155 ()23367403 (PubMedID)9781424441198 (ISBN)9781424441204 (ISBN)9781457717871 (ISBN)
    Conference
    34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2012), 28 August - 1 September 2012, San Diego, CA, USA
    Available from: 2012-10-03 Created: 2012-10-03 Last updated: 2018-01-12Bibliographically approved
    3. The effect of tissue heterogeneity and anisotropy on microdialysis of the deep brain
    Open this publication in new window or tab >>The effect of tissue heterogeneity and anisotropy on microdialysis of the deep brain
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Microdialysis of the basal ganglia was recently used to study changes of neurotransmitter levels in relation to deep brain stimulation (DBS). In order to estimate the anatomical origin of the microdialysis data, the maximum tissue volume of influence (TVImax) for a microdialysis catheter was simulated and visualized using the finite element method (FEM). In the current study the impact of brain heterogeneity and anisotropy on the TVImax was investigated, using diffusion tensor imaging (DTI) to create a second-order tensor model of the basal ganglia. The results were presented using descriptive statistics, indicating that the mean radius of the TVImax varied by up to 0.5 mm (n = 98444) for FEM simulations based on DTI compared to a homogeneous and isotropic reference model. The internal capsule and subthalamic area showed significantly higher anisotropy (p < 0.0001, n = 600) than the putamen and the globus pallidus, in accordance with theory. It was concluded that the size of the TVImax remained small enough to be relevant in relation to the anatomical structures of interest, and that local tissue properties should be accounted for when relating the microdialysis data to their anatomical targets.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-84276 (URN)
    Available from: 2012-10-03 Created: 2012-10-03 Last updated: 2016-05-04Bibliographically approved
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    Modeling and Simulation of Microdialysis in the Deep Brain Structures
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    omslag
  • 149.
    Diczfalusy, Elin
    et al.
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Wårdell, Karin
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    A diffusion tensor-based finite element model of microdialysis in the deep brain2015In: Computer Methods in Biomechanics and Biomedical Engineering, ISSN 1025-5842, E-ISSN 1476-8259, Vol. 18, no 2, p. 201-212Article in journal (Refereed)
    Abstract [en]

    Microdialysis of the basal ganglia was recently used to study neurotransmitter levels in relation to deep brain stimulation. In order to estimate the anatomical origin of the obtained data, the maximum tissue volume of influence (TVImax) for a microdialysis catheter was simulated using the finite element method. This study investigates the impact of brain heterogeneity and anisotropy on the TVImax using diffusion tensor imaging (DTI) to create a second-order tensor model of the basal ganglia. Descriptive statistics showed that the maximum migration distance for neurotransmitters varied by up to 55% (n = 98,444) for DTI-based simulations compared with an isotropic reference model, and the anisotropy differed between different targets in accordance with theory. The size of the TVImax was relevant in relation to the size of the anatomical structures of interest, and local tissue properties should be accounted for when relating microdialysis data to their anatomical targets.

  • 150.
    Diczfalusy, Elin
    et al.
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Didzar, Nil
    Östergötlands Läns Landsting, Local Health Care Services in Central Östergötland, Department of Neurology.
    Kullman, Anita
    Linköping University, Department of Clinical and Experimental Medicine, Clinical Chemistry. Linköping University, Faculty of Health Sciences.
    Åström, Mattias
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Zsigmond, Peter
    Linköping University, Department of Clinical and Experimental Medicine, Neurosurgery. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Reconstruction Centre, Department of Neurosurgery UHL.
    Wårdell, Karin
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Biochemical monitoring and simulation of the electric field during deep brain stimulation (oral)2010Conference paper (Other academic)
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