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  • 101.
    Brun, Anders
    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).
    Westin, Carl-Fredrik
    Laboratory of Mathematics in Imaging Harvard Medical School, Boston, USA.
    Herberthson, Magnus
    Linköping University, Department of Mathematics, Applied Mathematics. Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Fast manifold learning based on Riemannian normal coordinates2005In: Image Analysis: 14th Scandinavian Conference, SCIA 2005, Joensuu, Finland, June 19-22, 2005. Proceedings / [ed] Heikki Kalviainen, Jussi Parkkinen, Arto Kaarna., Springer Berlin/Heidelberg, 2005, p. 920-Conference paper (Refereed)
    Abstract [en]

    We present a novel method for manifold learning, i.e. identification of the low-dimensional manifold-like structure present in a set of data points in a possibly high-dimensional space. The main idea is derived from the concept of Riemannian normal coordinates. This coordinate system is in a way a generalization of Cartesian coordinates in Euclidean space. We translate this idea to a cloud of data points in order to perform dimension reduction. Our implementation currently uses Dijkstra’s algorithm for shortest paths in graphs and some basic concepts from differential geometry. We expect this approach to open up new possibilities for analysis of e.g. shape in medical imaging and signal processing of manifold-valued signals, where the coordinate system is “learned” from experimental high-dimensional data rather than defined analytically using e.g. models based on Lie-groups.

  • 102.
    Brun, Anders
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, The Institute of Technology.
    Westin, Carl-Fredrik
    Laboratory of Mathematics in Imaging, Harvard Medical School, Boston, MA, USA.
    Herberthson, Magnus
    Linköping University, Department of Mathematics, Applied Mathematics. Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, The Institute of Technology.
    Intrinsic and Extrinsic Means on the Circle -- a Maximum Likelihood Interpretation2007In: ICASSP 2007. IEEE International Conference on Acoustics, Speech and Signal Processing, 2007, New York, USA: IEEE , 2007, p. III-1053-III-1056Conference paper (Refereed)
    Abstract [en]

    For data samples in Rn, the mean is a well known estimator. When the data set belongs to an embedded manifold M in Rn, e.g. the unit circle in R2, the definition of a mean can be extended and constrained to M by choosing either the intrinsic Riemannian metric of the manifold or the extrinsic metric of the embedding space. A common view has been that extrinsic means are approximate solutions to the intrinsic mean problem. This paper study both means on the unit circle and reveal how they are related to the ML estimate of independent samples generated from a Brownian distribution. The conclusion is that on the circle, intrinsic and extrinsic means are maximum likelihood estimators in the limits of high SNR and low SNR respectively

  • 103.
    Brun, Anders
    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).
    Westin, Carl-Fredrik
    Lab of Mathematics in Imaging Harvard Medical School, Boston, USA.
    Herberthson, Magnus
    Linköping University, Department of Mathematics, Applied Mathematics. Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    LOGMAP: Preliminary results using a new method for manifold learning2005In: Symposium on Image Analysis SSBA,2005, 2005, p. 101-105Conference paper (Other academic)
  • 104.
    Brun, Anders
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Westin, Carl-Fredrik
    Harvard Medical School Boston.
    Herberthson, Magnus
    Linköping University, The Institute of Technology. Linköping University, Department of Mathematics, Applied Mathematics.
    Knutsson, Hans
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Sample Logmaps - Intrinsic processing of empirical manifold data2006In: SSBA Symposium on Image Analysis,2006, 2006, p. 13-16Conference paper (Other academic)
  • 105.
    Burger, Gerard
    et al.
    Symbiant Pathol Expert Centre, Netherlands; University of Amsterdam, Netherlands.
    Abu-Hanna, Ameen
    University of Amsterdam, Netherlands.
    de Keizer, Nicolette
    University of Amsterdam, Netherlands.
    Cornet, Ronald
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. University of Amsterdam, Netherlands.
    Natural language processing in pathology: a scoping review2016In: Journal of Clinical Pathology, ISSN 0021-9746, E-ISSN 1472-4146, Vol. 69, no 11, p. 949-955Article, review/survey (Refereed)
    Abstract [en]

    Background Encoded pathology data are key for medical registries and analyses, but pathology information is often expressed as free text. Objective We reviewed and assessed the use of NLP (natural language processing) for encoding pathology documents. Materials and methods Papers addressing NLP in pathology were retrieved from PubMed, Association for Computing Machinery (ACM) Digital Library and Association for Computational Linguistics (ACL) Anthology. We reviewed and summarised the study objectives; NLP methods used and their validation; software implementations; the performance on the dataset used and any reported use in practice. Results The main objectives of the 38 included papers were encoding and extraction of clinically relevant information from pathology reports. Common approaches were word/phrase matching, probabilistic machine learning and rule-based systems. Five papers (13%) compared different methods on the same dataset. Four papers did not specify the method(s) used. 18 of the 26 studies that reported F-measure, recall or precision reported values of over 0.9. Proprietary software was the most frequently mentioned category (14 studies); General Architecture for Text Engineering (GATE) was the most applied architecture overall. Practical system use was reported in four papers. Most papers used expert annotation validation. Conclusions Different methods are used in NLP research in pathology, and good performances, that is, high precision and recall, high retrieval/removal rates, are reported for all of these. Lack of validation and of shared datasets precludes performance comparison. More comparative analysis and validation are needed to provide better insight into the performance and merits of these methods.

  • 106.
    Bäck, David
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Neural Network Gaze Tracking using Web Camera2006Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Gaze tracking means to detect and follow the direction in which a person looks. This can be used in for instance human-computer interaction. Most existing systems illuminate the eye with IR-light, possibly damaging the eye. The motivation of this thesis is to develop a truly non-intrusive gaze tracking system, using only a digital camera, e.g. a web camera.

    The approach is to detect and track different facial features, using varying image analysis techniques. These features will serve as inputs to a neural net, which will be trained with a set of predetermined gaze tracking series. The output is coordinates on the screen.

    The evaluation is done with a measure of accuracy and the result is an average angular deviation of two to four degrees, depending on the quality of the image sequence. To get better and more robust results, a higher image quality from the digital camera is needed.

  • 107.
    Bågenholm, Per
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Anderskär, Kristina
    IMT .
    Gill, Hans
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Jönsson, K Å
    Dept Medicine University Hospital, Linköping.
    Wigertz, Ove
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Adding decision support to a clinical information system1994In: Technology and Health Care, ISSN 0928-7329, Vol. 1, p. 245-251Article in journal (Refereed)
  • 108.
    Bårman, Håkan
    et al.
    n/a.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Granlund, Gösta H.
    Linköping University, Department of Electrical Engineering, Computer Vision . Linköping University, The Institute of Technology.
    Using Principal Direction Estimates for Shape and Acceleration Description1991In: Proceedings of the SSAB Symposium on Image Analysis: Stockholm, 1991Conference paper (Refereed)
  • 109.
    Caesar, Jenny
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Segmentation of the Brain from MR Images2005Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    KTH, Division of Neuronic Engineering, have a finite element model of the head. However, this model does not contain detailed modeling of the brain. This thesis project consists of finding a method to extract brain tissues from T1-weighted MR images of the head. The method should be automatic to be suitable for patient individual modeling.

    A summary of the most common segmentation methods is presented and one of the methods is implemented. The implemented method is based on the assumption that the probability density function (pdf) of an MR image can be described by parametric models. The intensity distribution of each tissue class is modeled as a Gaussian distribution. Thus, the total pdf is a sum of Gaussians. However, the voxel values are also influenced by intensity inhomogeneities, which affect the pdf. The implemented method is based on the expectation-maximization algorithm and it corrects for intensity inhomogeneities. The result from the algorithm is a classification of the voxels. The brain is extracted from the classified voxels using morphological operations.

  • 110.
    Cammoun, L.
    et al.
    Signal Processing Institute Ecole Polytechnigue Fédérale de Lausanne Switserland.
    Castano-Moraga, C.A.
    University of Las Palmas de Gran Canaria.
    Munoz-Moreno, E.
    Univ. de Valladolid, Spain.
    Sosa-Cabrera, D.
    University of Las Palmas de Gran Canaria.
    Acar, B.
    University Istanbul.
    Rodriguez-Florido, M.A.
    University of Las Palmas de Gran Canaria.
    Brun, Anders
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Thiran, J.P.
    Signal Processing Institute Ecole Polytechnigue Fédérale de Lausanne Switserland.
    A Review of Tensors and Tensor Signal Processing2009In: Tensors in Image Processing and Computer Vision / [ed] S. Aja-Fernandez, R. de Luis Garcia, D. Tao, and X. Li, Springer London, 2009, p. 1-32Chapter in book (Refereed)
    Abstract [en]

    Tensors have been broadly used in mathematics and physics, since they are a generalization of scalars or vectors and allow to represent more complex properties. In this chapter we present an overview of some tensor applications, especially those focused on the image processing field. From a mathematical point of view, a lot of work has been developed about tensor calculus, which obviously is more complex than scalar or vectorial calculus. Moreover, tensors can represent the metric of a vector space, which is very useful in the field of differential geometry. In physics, tensors have been used to describe several magnitudes, such as the strain or stress of materials. In solid mechanics, tensors are used to define the generalized Hooke’s law, where a fourth order tensor relates the strain and stress tensors. In fluid dynamics, the velocity gradient tensor provides information about the vorticity and the strain of the fluids. Also an electromagnetic tensor is defined, that simplifies the notation of the Maxwell equations. But tensors are not constrained to physics and mathematics. They have been used, for instance, in medical imaging, where we can highlight two applications: the diffusion tensor image, which represents how molecules diffuse inside the tissues and is broadly used for brain imaging; and the tensorial elastography, which computes the strain and vorticity tensor to analyze the tissues properties. Tensors have also been used in computer vision to provide information about the local structure or to define anisotropic image filters.

  • 111.
    Carlsson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Methods and computer based tools for handling medical terminologies and classifications2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Classifications, terminology and terminology services are important in the field of medical informatics. They are needed when building applications such as Computer based Patient Record systems (CPRs). Even though many classifications, nomenclatures and terminology systems have been constructed to this end, e .g. ICD, MeSH and SNOMED, no single system has, so far, covered medicine in its entirety. Several of the aforementioned constructs have grown to the extent that manual maintenance can no longer cope, thus computer based tools are needed for this task.

    The main objective of this thesis is to present some computer based terminology tools that have been constructed to facilitate part of the work of building sound terminologies and application systems. The usefulness of such terminologies, terminology tools as well as the importance of being able to integrate the terminology have been reviewed and are discussed. Moreover tools (from GALEN) for maintenance and developme nt of classilications are evaluated.

    Two terminology tools are presented that aim to facilitate the access to and the use of terminology and terminology services. One tool is built on a proposal for a concept oriented Swedish national terminology data base model (Spriterm). The other tool is a dedicated client (KOMANTIS) to the GALEN terminology server (TeS) developed as a deliverable within the European GALEN project. It will facilitate the integration of terminologies between the information system and the knowledge base when building Decision Support Systems (DSS).

    List of papers
    1. Development of a terminology management system for the Swedish healthcare sector
    Open this publication in new window or tab >>Development of a terminology management system for the Swedish healthcare sector
    1996 (English)In: Studies in Health Technology and Informatics, Volume 34: Medical Informatics Europe ’96, Amsterdam: IOS Press , 1996, p. 232-235Conference paper, Published paper (Refereed)
    Abstract [en]

    This paper describes the ongoing work of creating and building a Swedish national terminology database. The terminology management system herein is a prototype, built in ACCESS™. Still it addresses some important issues concerning terminology management such as the data model used for representing concepts and terms, and multiple inheritance is discussed in relation to relational databases.

    Place, publisher, year, edition, pages
    Amsterdam: IOS Press, 1996
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-31352 (URN)10.3233/978-1-60750-878-6-232 (DOI)17118 (Local ID)17118 (Archive number)17118 (OAI)
    Conference
    MIE 96, Thirteenth International Congress, August 19-22 1996 Copenhagen Denmark
    Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2013-02-25
    2. Design and application of a terminology management system
    Open this publication in new window or tab >>Design and application of a terminology management system
    1998 (English)In: Studies in Health Technology and Informatics, Volume 52: MEDINFO '98 / [ed] Cesnik, B., McCray, A.T., Scherrer, J.R., Australia: IOS Press , 1998, p. 207-211Conference paper, Published paper (Refereed)
    Abstract [en]

    A Swedish data model for handling terminology, Spriterm, is presented in this paper. A prototype terminology management system, using the Spriterm data model in also described. This prototype is implemented is Microsoft ACCESS. Furthermore, two other applications using this prototype as a base are introduced. One World Wide Web based application, and a data dictionary.

    Place, publisher, year, edition, pages
    Australia: IOS Press, 1998
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-29899 (URN)10.3233/978-1-60750-896-0-207 (DOI)15320 (Local ID)978-90-5199-407-0 (ISBN)15320 (Archive number)15320 (OAI)
    Conference
    MEDINFO '98, Aug 14-21, Seoul, South Korea
    Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2013-02-25
    3. Terminology support for development of sharable knowledge modules
    Open this publication in new window or tab >>Terminology support for development of sharable knowledge modules
    1996 (English)In: Informatics for Health and Social Care, ISSN 1753-8157, E-ISSN 1753-8165, Vol. 21, no 3, p. 207-214Article in journal (Refereed) Published
    Abstract [en]

    Lack of an agreed infrastructure for terminology is identified as one of the major barriers to interchange of knowledge modules and integration of knowledge bases with other clinical information systems. The goal of the GALEN project is to bridge this gap between different terminology systems through the construction of a terminology server, which is based on a rich conceptual model with mapping facilities to natural language expressions and coding schemas. The long term goal is to support communication between medical information systems. Arden Syntax is a standard format for the creation of knowledge modules, with sharability as one of the main objectives. Since Arden Syntax is based on a data-driven approach, the data items used need to be adapted to locally available terminology. The GALEN approach appears to be complementary to Arden Syntax and to the development of sharable knowledge modules. The major theme of this paper is utilization of the GALEN terminology server for knowledge module authoring. Two systems are presented, a knowledge base manager and a client to the terminology server, allowing the user to navigate in the semantic network and to import concept definitions and terms into the knowledge modules. The benefit of the terminology services is discussed.

    Keywords
    Terminology services, Knowledge authoring, Knowledge sharing, Arden Syntax
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-31359 (URN)10.3109/14639239609025358 (DOI)17125 (Local ID)17125 (Archive number)17125 (OAI)
    Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2017-12-13
    4. Modelling and reclassification of surgical procedures: experiences from the use of GALEN methods in the domain of thoracic surgery
    Open this publication in new window or tab >>Modelling and reclassification of surgical procedures: experiences from the use of GALEN methods in the domain of thoracic surgery
    2000 (English)In: Medical informatics and the Internet in medicine (Print), ISSN 1463-9238, E-ISSN 1464-5238, Vol. 25, no 2, p. 109-122Article in journal (Refereed) Published
    Abstract [en]

    This paper reports on experiences fromthe evaluation of GALEN methods for mapping of follow-up categories in the domain of thoracic surgery to an existing classification of surgical procedures. The mapping of the aggregated levels or groups of thoracic procedures presents a genuine problem in relation to strict hierarchical classifications, since the follow-up categories do not necessarily fit in the pre-set structure of the classification. Experiences from modelling of the traditional classification and of the follow-up categories are reported, and an analysis of the results is presented along with a discussion of opportunities and potential problems and pitfalls when applying GALEN models and tools.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-29754 (URN)10.1080/14639230050058293 (DOI)15159 (Local ID)15159 (Archive number)15159 (OAI)
    Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2017-12-13
    5. Classification of procedures in the domain of thoracic surgery: a study of relibility in coding
    Open this publication in new window or tab >>Classification of procedures in the domain of thoracic surgery: a study of relibility in coding
    2001 (English)In: Journal of medical systems, ISSN 0148-5598, E-ISSN 1573-689X, Vol. 25, no 1, p. 47-61Article in journal (Refereed) Published
    Abstract [en]

    This paper relates a study of reliability of coding of surgical procedures in the domain of thoracic surgery. The reliability measured is inter-coder variability in form of agreement. Four classifications were used by four physicians on 100 patient cases. The classifications, having differing granularity and structure, were analyzed using a statistical method (kappa). These results are discussed and related to the differences between the classifications. One of the topics for discussion is how the granularity affects the degree of agreement, coupled to the usefulness of the classification. Also the concept of using formal methods for representing classifications is discussed, how this will affect how classifications are designed and used.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:liu:diva-29560 (URN)10.1023/A:1005636432502 (DOI)14934 (Local ID)14934 (Archive number)14934 (OAI)
    Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2017-12-13
  • 112.
    Carlsson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Tools for providing terminology services in health care computing1997Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Terminology and terminology services are increasingly important in building medical informatics applications like Computerbased Patient Record systems (CPR). Many classifications, nomenclatures and terminology systems have been constructed to this end i. a. ICD, MeSH and SNOMED. So far no single system has covered medicine in its entirety and particularly have they not been suitable for building computerbased applications and handling.

    The arrival of computer technology has led to new, more advanced terminology systems. The combination of these new terminology systems with knowledge representation vehicles such as Arden Syntax constitutes an important part of the process of developing efficient methods and systems for information handling including decision support and communication of meaning within health care.

    The main objective of the thesis is to present some computer based terminology tools that have been constructed to facilitate part of the work of building sound terminologies and application systems. The usefulness of such terminologies, terminology tools and the importance of being able to integrate the terminology have been reviewed and are discussed.

    Two terminology tools are presented that aims at facilitating the access to and the use of terminology and terminology services. One tool is built on the concept oriented Swedish national terminology data base model SpriTerm and provides browsing and editing facilities of concepts and concept spaces of vocabularies. Also the motivations behind the SpriTerm model are discussed.

    The other tool is a dedicated client (KOMANTIS) to the GALEN terminology server (TeS) developed as a deliverable within the European GALEN project. It will facilitate the integration of terminologies between an information system, and the knowledge base when building Decision Support Systems (DSS). The user can navigate through KOMANTIS and select the pertinent attributes for integrating, for example the DSS and the CPR.

  • 113.
    Carlsson, Mats
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Karlsson, Daniel
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Åhlfeldt, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Wigertz, Ove
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Design and application of a terminology management system1998In: Studies in Health Technology and Informatics, Volume 52: MEDINFO '98 / [ed] Cesnik, B., McCray, A.T., Scherrer, J.R., Australia: IOS Press , 1998, p. 207-211Conference paper (Refereed)
    Abstract [en]

    A Swedish data model for handling terminology, Spriterm, is presented in this paper. A prototype terminology management system, using the Spriterm data model in also described. This prototype is implemented is Microsoft ACCESS. Furthermore, two other applications using this prototype as a base are introduced. One World Wide Web based application, and a data dictionary.

  • 114.
    Carlsson, Mats
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Löfström, Lars
    Linköping University, Faculty of Health Sciences.
    Rogers, Jeremy
    Medical Informatics Group, Department of Computer Science, University of Manchester, UK.
    Åhlfeldt, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Modelling and reclassification of surgical procedures: experiences from the use of GALEN methods in the domain of thoracic surgery2000In: Medical informatics and the Internet in medicine (Print), ISSN 1463-9238, E-ISSN 1464-5238, Vol. 25, no 2, p. 109-122Article in journal (Refereed)
    Abstract [en]

    This paper reports on experiences fromthe evaluation of GALEN methods for mapping of follow-up categories in the domain of thoracic surgery to an existing classification of surgical procedures. The mapping of the aggregated levels or groups of thoracic procedures presents a genuine problem in relation to strict hierarchical classifications, since the follow-up categories do not necessarily fit in the pre-set structure of the classification. Experiences from modelling of the traditional classification and of the follow-up categories are reported, and an analysis of the results is presented along with a discussion of opportunities and potential problems and pitfalls when applying GALEN models and tools.

  • 115.
    Carlsson, Mats
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Löfström, Lars
    Linköping University, Faculty of Health Sciences.
    Åhlfeldt, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Classification of procedures in the domain of thoracic surgery: a study of relibility in coding2001In: Journal of medical systems, ISSN 0148-5598, E-ISSN 1573-689X, Vol. 25, no 1, p. 47-61Article in journal (Refereed)
    Abstract [en]

    This paper relates a study of reliability of coding of surgical procedures in the domain of thoracic surgery. The reliability measured is inter-coder variability in form of agreement. Four classifications were used by four physicians on 100 patient cases. The classifications, having differing granularity and structure, were analyzed using a statistical method (kappa). These results are discussed and related to the differences between the classifications. One of the topics for discussion is how the granularity affects the degree of agreement, coupled to the usefulness of the classification. Also the concept of using formal methods for representing classifications is discussed, how this will affect how classifications are designed and used.

  • 116.
    Carlsson, Mats
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Rogers, Jeremy
    University of Manchester, UK .
    Åhlfeldt, Hans
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Aggregation and reclassification - Assessment of GALEN methods in the domain of thoracic surgery1999In: AIA99,1999, Philadelphia: Hanley & Belfus Inc , 1999, p. 32-Conference paper (Refereed)
  • 117.
    Carlsson, Mats
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Wigertz, Ove
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Junford, A.
    Swedish Institute for Health Services Development, Stockholm, Sweden.
    Wallin, S-B.
    Swedish Institute for Health Services Development, Stockholm, Sweden.
    Development of a terminology management system for the Swedish healthcare sector1996In: Studies in Health Technology and Informatics, Volume 34: Medical Informatics Europe ’96, Amsterdam: IOS Press , 1996, p. 232-235Conference paper (Refereed)
    Abstract [en]

    This paper describes the ongoing work of creating and building a Swedish national terminology database. The terminology management system herein is a prototype, built in ACCESS™. Still it addresses some important issues concerning terminology management such as the data model used for representing concepts and terms, and multiple inheritance is discussed in relation to relational databases.

  • 118.
    Carlsson, Mats
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Åhlfeldt, Hans
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Thurin, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Wigertz, Ove
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Knowledge module authoring with terminolgy support1995In: AMIA Symposium on Coputer Applications in Medical Care,1995, Hanley & belfus , 1995, p. 969-Conference paper (Refereed)
  • 119.
    Carlsson, Mats
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Åhlfeldt, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Thurin, Anders
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Wigertz, Ove
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Terminology support for development of sharable knowledge modules1996In: Informatics for Health and Social Care, ISSN 1753-8157, E-ISSN 1753-8165, Vol. 21, no 3, p. 207-214Article in journal (Refereed)
    Abstract [en]

    Lack of an agreed infrastructure for terminology is identified as one of the major barriers to interchange of knowledge modules and integration of knowledge bases with other clinical information systems. The goal of the GALEN project is to bridge this gap between different terminology systems through the construction of a terminology server, which is based on a rich conceptual model with mapping facilities to natural language expressions and coding schemas. The long term goal is to support communication between medical information systems. Arden Syntax is a standard format for the creation of knowledge modules, with sharability as one of the main objectives. Since Arden Syntax is based on a data-driven approach, the data items used need to be adapted to locally available terminology. The GALEN approach appears to be complementary to Arden Syntax and to the development of sharable knowledge modules. The major theme of this paper is utilization of the GALEN terminology server for knowledge module authoring. Two systems are presented, a knowledge base manager and a client to the terminology server, allowing the user to navigate in the semantic network and to import concept definitions and terms into the knowledge modules. The benefit of the terminology services is discussed.

  • 120.
    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.

  • 121.
    Chellappa, Rama
    et al.
    Department of Electrical and Computer Engineering, University of Maryland, USA.
    Heyden, AndersLund University, Sweden.Laurendeau, DenisUniversité Laval, Canada.Felsberg, MichaelLinköping University, Department of Electrical Engineering, Computer Vision. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).Borga, MagnusLinköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Arts and Sciences. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Special issue on ICPR 2014 awarded papers2016Collection (editor) (Refereed)
    Abstract [en]

    We, the Guest Editors of this special issue of Pattern Recognition Letters are pleased to share these contributions with you. The papers included here are based on work from the 22nd International Conference on Pattern Recognition (IAPR) in Stockholm, Sweden, held August 24–28, 2014. The papers selected for this special issue were those winning one of the IAPR awards, as well as one paper by a former student of the winner of the KS Fu Prize, Prof. Jitendra Malik. Taken together, this body of work represents some of the finest research being conducted by the IAPR community worldwide, it builds on a rich legacy of accomplishment by the entire community, and it offers a view to the future, to where we are going as a scientific community.

    For each of the award-winning papers, the authors were asked to revise and extend their contributions to full journal length and to provide true added value vis-à-vis the original conference submission. In some cases, the authors elected to modify the titles slightly, and in some cases the list of authors has also been modified. The resulting manuscripts were sent out for full review by a different set of referees than those who reviewed the conference versions. The process, including required revisions, was in accordance with the standing editorial policy of Pattern Recognition Letters, resulting in the final versions accepted and appearing here. These are thoroughly vetted, high-caliber scientific contributions.

    It has been our honor to serve as Guest Editors for this special issue. We would like to thank the Editors of Pattern Recognition Letters for allowing us this opportunity. We are especially grateful to Dr. Gabriella Sanniti di Baja for her enthusiasm, support, and her willingness to keep prodding us along to bring the special issue through to completion. We would also like to thank all of those who reviewed the papers, both originally for the conference and subsequently for the journal, and those who served on the ICPR awards and KS Fu Prize committees.

    Finally, we express our heartfelt gratitude to all of the authors for taking the time to prepare these versions for our collective enlightenment, sharing their knowledge, innovation, and discoveries with the rest of us.

  • 122.
    Chen, Rong
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Garde, Sebastian
    Ocean Informatics UK, London, UK.
    Beale, Thomas
    Ocean Informatics UK, London, UK.
    Nyström, Mikael
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Karlsson, Daniel
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Klein, Gunnar O.
    Karolinska Institutet, Sweden.
    Åhlfeldt, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    An Archetype-based Testing Framework2008In: EHEALTH BEYOND THE HORIZON: GET IT THERE / [ed] Andersen, SK; Klein, GO; Schulz, S; Aarts, J; Mazzoleni, MC, Amsterdam: IOS Press, 2008, Vol. 136, p. 401-406Conference paper (Refereed)
    Abstract [en]

    With the introduction of EHR two-level modelling and archetype methodologies pioneered by openEHR and standardized by CEN/ISO, we are one step closer to semantic interoperability and future-proof adaptive healthcare information systems. Along with the opportunities, there are also challenges. Archetypes provide the full semantics of EHR data explicitly to surrounding systems in a platform-independent way, yet it is up to the receiving system to interpret the semantics and process the data accordingly. In this paper we propose a design of an archetype-based platform-independent testing framework for validating implementations of the openEHR archetype formalism as a means of improving quality and interoperability of EHRs.

  • 123.
    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.

  • 124.
    Chen, Rong
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Klein, Gunnar
    Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
    The openEHR Java Reference Implementation Project2007In: Proceedings of the 12th World Congress onHealth (Medical) Informatics / [ed] K.A. Kuhn, J.R. Warren and T.-Y. Leong, IOS Press , 2007, p. 58-62Conference paper (Refereed)
    Abstract [en]

    The openEHR foundation has developed an innovative design for interoperable and future-proof Electronic Health Record (EHR) systems based on a dual model approach with a stable reference information model complemented by archetypes for specific clinical purposes.

    A team from Sweden has implemented all the stable specifications in the Java programming language and donated the source code to the openEHR foundation. It was adopted as the openEHR Java Reference Implementation in March 2005 and released under open source licenses. This encourages early EHR implementation projects around the world and a number of groups have already started to use this code.

    The early Java implementation experience has also led to the publication of the openEHR Java Implementation Technology Specification. A number of design changes to the specifications and important minor corrections have been directly initiated by the implementation project over the last two years. The Java Implementation has been important for the validation and improvement of the openEHR design specifications and provides building blocks for future EHR systems.

  • 125.
    Chen, Rong
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Klein, Gunnar O
    Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
    Sundvall, Erik
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Karlsson, Daniel
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Åhlfeldt, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Archetype-based conversion of EHR content models: pilot experience with a regional EHR system2009In: BMC Medical Informatics and Decision Making, ISSN 1472-6947, E-ISSN 1472-6947, Vol. 9, no 33Article in journal (Refereed)
    Abstract [en]

    Background: Exchange of Electronic Health Record (EHR) data between systems from different suppliers is a major challenge. EHR communication based on archetype methodology has been developed by openEHR and CEN/ISO. The experience of using archetypes in deployed EHR systems is quite limited today. Currently deployed EHR systems with large user bases have their own proprietary way of representing clinical content using various models. This study was designed to investigate the feasibility of representing EHR content models from a regional EHR system as openEHR archetypes and inversely to convert archetypes to the proprietary format. Methods: The openEHR EHR Reference Model (RM) and Archetype Model (AM) specifications were used. The template model of the Cambio COSMIC, a regional EHR product from Sweden, was analyzed and compared to the openEHR RM and AM. This study was focused on the convertibility of the EHR semantic models. A semantic mapping between the openEHR RM/AM and the COSMIC template model was produced and used as the basis for developing prototype software that performs automated bidirectional conversion between openEHR archetypes and COSMIC templates. Results: Automated bi-directional conversion between openEHR archetype format and COSMIC template format has been achieved. Several archetypes from the openEHR Clinical Knowledge Repository have been imported into COSMIC, preserving most of the structural and terminology related constraints. COSMIC templates from a large regional installation were successfully converted into the openEHR archetype format. The conversion from the COSMIC templates into archetype format preserves nearly all structural and semantic definitions of the original content models. A strategy of gradually adding archetype support to legacy EHR systems was formulated in order to allow sharing of clinical content models defined using different formats. Conclusion: The openEHR RM and AM are expressive enough to represent the existing clinical content models from the template based EHR system tested and legacy content models can automatically be converted to archetype format for sharing of knowledge. With some limitations, internationally available archetypes could be converted to the legacy EHR models. Archetype support can be added to legacy EHR systems in an incremental way allowing a migration path to interoperability based on standards.

  • 126.
    Chowdhury, Shamsul
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Bodemar, Göran
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Molecular and Clinical Medicine, Gastroenterology and Hepatology. Östergötlands Läns Landsting, Centre for Medicine, Department of Endocrinology and Gastroenterology UHL.
    Haug, Peter
    Utah University USA.
    Babic, Ankica
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Wigertz, Ove
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Methods for knowledge extraction from clinical database on liver diseases1991In: Computers and biomedical research, ISSN 0010-4809, E-ISSN 1090-2368, Vol. 24, p. 530-548Article in journal (Refereed)
  • 127.
    Chowdhury, Shamsul I.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
    Computer-based support for knowledge extraction from clinical databases1990Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is devoted to aspects related to the analysis and interpretation of medical data thus allowing knowledge extraction from medical databases. The difficulties with traditional approaches for data analysis and interpretation by people less proficient in statistics are well known. An attempt has been made to identify different stages in the processes of data analysis and interpretation where this category of users might need help and to identify how this help could best be provided (studies I, II, III). In this work artificial intelligence approaches have been used as remedies to improve user-friendliness as well as power and effectiveness of statistical software in respect to data analysis strategies. Prototype implementations based on these approaches are presented and discussed. Issues pertaining to the evaluation of decision support systems m medicine have been identified and discussed in detail (study IV).

    Knowledge in a knowledge-based system for decision support is generally acquired from experts and the literature. Knowledge can also be effectively extracted from a database of patient observations and from interpretation of those observations. The resulting system would be more accurate in the latter case, especially if it is intended to operate in decision support in the same clinical setting.

    The studies V and VI were conducted to show how retrospectively collected data could be utilized for the purpose of knowledge extraction. More traditional data analysis approaches (study V) were used to analyze a database on liver diseases. The data material used in the study was collected in the HELP system as a routine part of patient care. The main issues involved were detection of outliers and treatment of missing values in order to facilitate utilization of this kind of database for eventual knowledge extraction. In Study V, statistical techniques including discriminant analysis and artificial intelligence approaches such asinductive learning, were used. The 'K nearest neighbor' technique was found to be an easy and acceptable method for estimating missing values when the database contained only a few missing values for each object in the database. Discriminant analysis was found to be a good method for classifying a patient, based on a set of variables, into two or more disease classes. The results show that when discriminant analysis was applied to two groups based on a relatively large number (19) of variables, then only a few (3) of the variables accounted for a high percentage of correct classifications.

    The knowledge-based approach for data analysis and interpretation used in (study III) was applied to a large database (study VI). The main emphasis was to study the feasibility of the approach in exploring a large patient record system. The data material was taken from Kronan Health Center - a primary health care center in suburban Stockholm with a patient database consisting of about 14,000 medical records. The analysis was carried out to test the hypothesis of a possible causation between hypertension and diabetes. The results of this study support the assumption that there is a relationship between diabetes and hypertension but the question of the direction of this relationship remained unsolved, as did the question of direct causality. On the other hand, the results of this study are in accordance with the hypothesis of a common metabolic syndrome. The results arrived at by the analysis method (multivariate tabular analysis) utilized by the system are, moreover in accordance with another statistical method (log linear analysis). This also supports the approach taken in the knowledge-based system.

  • 128.
    Chowdhury, Shamsul
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Linnarsson, Rolf
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Wallgren, Anders
    Dept of Statistics Sween Örebro.
    Wallgren, Britt
    Dept Statistics Sweden Örebro.
    Wigertz, Ove
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Extracting knowledge from a large primary health care database using a knowledge-based statistical approach1990In: Journal of medical systems, ISSN 0148-5598, E-ISSN 1573-689X, Vol. 14, no 4, p. 213-225Article in journal (Refereed)
  • 129.
    Chowdhury, Shamsul
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Mathiesen, Ulrik
    Oskarshamns sjukhus .
    Krusinska, Ewa
    Technical University of Wroclaw, Poland .
    Franzén, Lennart
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Neuroscience and Locomotion, Pathology. Östergötlands Läns Landsting, Centre for Laboratory Medicine, Department of Clinical Pathology and Clinical Genetics.
    Wigertz, Ove
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Bodemar, Göran
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Molecular and Clinical Medicine, Gastroenterology and Hepatology. Östergötlands Läns Landsting, Centre for Medicine, Department of Endocrinology and Gastroenterology UHL.
    Design and delivery of information resources and knowledge bases for the diagnosis and managementof liver disorders1994In: ANZIIS-94,1994, Brisbane: IEEE , 1994Conference paper (Refereed)
  • 130.
    Chowdhury, Shamsul
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Wigertz, Ove
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Artificial Intelligence methods in data analysis and interpretation1990In: Knowledge, Data and Computer-assisted Decisions / [ed] Martin Schader, Wolfgang Gaul, Berlin: Springer Verlag , 1990, p. 199-208Chapter in book (Other academic)
  • 131.
    Chowdhury, Shamsul
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Wigertz, Ove
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Sundgren, Bo
    Stockholm School of Econimics .
    A knowledge-based system for data analysis and interpretation1989In: Methods of Information in Medicine, ISSN 0026-1270, Vol. 28Article in journal (Refereed)
  • 132.
    Collste, Göran
    et al.
    Linköping University, Faculty of Arts and Sciences. Linköping University, Department of Religion and Culture, Center for Applied Ethics.
    Shahsavar, Nosrat
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Gill, Hans
    Linköping University, The Institute of Technology. Linköping University, Department of Biomedical Engineering, Medical Informatics.
    A decision support system for diabetes care: Ethical aspects1999In: Methods of Information in Medicine, ISSN 0026-1270, Vol. 38, p. 313-316Article in journal (Refereed)
  • 133.
    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.

  • 134.
    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.

  • 135.
    Cros, Olivier
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Image Analysis and Visualization of the Human Mastoid Air Cell System2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    From an engineering background, it is often believed that the human anatomy has already been fully described. Radiology has greatly contributed to understand the inside of the human body without surgical intervention. Despite great advances in clinical CT scanning, image quality is still related to a limited amount X-ray exposure for the patient safety. This limitation prevents fine anatomical structures to be visible and, more importantly, to be detected. Where such modality is of great advantage for screening patients, extracting parameters like surface area and volume implies the bone structure to be large enough in relation to the scan resolution.

    The mastoid, located in the temporal bone, houses an air cell system whose cells have a variation in size that can go far below current conventional clinical CT scanner resolution. Therefore, the mastoid air cell system is only partially represented on a CT scan. Any statistical analysis will be biased towards air cells of smaller size. To allow a complete representation of the mastoid air cell system, a micro-CT scanner is more adequate. Micro-CT scanning uses approximately the same amount of X-rays but for a much longer exposure time compared to what is normally allowed for patients. Human temporal bone specimens are therefore necessary when using such scanning method. Where the conventional clinical CT scanner lacks level of minutes details, micro-CT scanning provides an overwhelming amount of fine details.

    Prior to any image analysis of medical data, visualization of the data is often needed to learn how to extract the structures of interest for further processing. Visualization of micro-CT scans is of no exception. Due to the high resolution nature of the data, visualization of such data not only requires modern and powerful computers, but also necessitates a tremendous amount of time to adjust the hiding of irrelevant structures, to find the correct orientation, while emphasising the structure of interest. Once the quality of the data has been assessed, and a strategy for the image processing has been decided, the image processing can start, to in turn extract metrics such as the surface area or volume and draw statistics from it. The temporal bone being one of the most complex in the human body, visualization of micro-CT scanning of this bone awakens the curiosity of the experimenter, especially with the correct visualization settings.

    This thesis first presents a statistical analysis determining the surface area to volume ratio of the mastoid air cell system of human temporal bone, from micro-CT scanning using methods previously applied for conventional clinical CT scannings. The study compared current resul s with previous studies, with successive downsampling the data down to a resolution found in conventional clinical CT scanning. The results from the statistical analysis showed that all the small mastoid air cells, that cannot be detected in conventional clinical CT scans, do heavily contribute to the estimation of the surface area, and in consequence to the estimation of the surface area to volume ratio by a factor of about 2.6. Such a result further strengthens the idea of the mastoid to play an active role in pressure regulation and gas exchange.

    Discovery of micro-channels through specific use of a non-traditional transfer function was then reported, where a qualitative and a quantitative preanalysis was performed are described. To gain more knowledge about these micro-channels, a local structure tensor analysis was applied where structures are described in terms of planar, tubular, or isotropic structures. The results from this structural tensor analysis, also reported in this thesis, suggest these micro-channels to potentially be part of a more complex framework, which hypothetically would provide a separate blood supply for the mucosa lining the mastoid air cell system.

    List of papers
    1. Determination of the mastoid surface area and volume based on micro-CT scanning of human temporal bone: Geometrical parameters dependence on scanning resolutions
    Open this publication in new window or tab >>Determination of the mastoid surface area and volume based on micro-CT scanning of human temporal bone: Geometrical parameters dependence on scanning resolutions
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    2016 (English)In: Hearing Research, ISSN 0378-5955, E-ISSN 1878-5891, Vol. 340, p. 127-134Article in journal (Other academic) Published
    Abstract [en]

    The mastoid air cell system (MACS) with its large complex of interconnected air cells reflects an enhanced surface area (SA) relative to its volume (V), which may indicate that the MACS is adapted to gas exchange and has a potential role in middle ear pressure regulation. Thus, these geometric parameters of the MACS have been studied by high resolution clinical CT scanning. However, the resolution of these scans is limited to a voxel size of around 0.6 mm in all dimensions, and so, the geometrical parameters are also limited. Small air cells may appear below the resolution and cannot be detected. Such air cells may contribute to a much higher SA than the V, and thus, also the SA/V ratio. More accurate parameters are important for analysis of the function of the MACS including physiological modeling.

    Our aim was to determine the SA, V, and SA/V ratio in MACS in human temporal bones at highest resolution by using micro-CT-scanning. Further, the influence of the resolution on these parameters was investigated by downsampling the data. Eight normally aerated temporal bones were scanned at the highest possible resolution (30-60 μm). The SA was determined using a triangular mesh fitted onto the segmented MACS. The V was determined by summing all the voxels containing air. Downsampling of the original data was applied four times by a factor of 2.

    The mean SA was 194 cm2, the mean V was 9 cm3, and the mean SA/V amounted to 22 cm-1. Decreasing the resolution resulted in a non-linear decrement of SA and SA/V, whereas V was mainly independent of the resolution.

    The current study found significantly higher SA and SA/V compared with previous studies using clinical CT scanning at lower resolutions. These findings indicate a separate role of the MACS compared with the tympanum, and the results are important for a more accurate modeling of the middle ear physiology.

    Keywords
    Mastoid air cells; medical imaging; micro-CT; surface area; volume
    National Category
    Radiology, Nuclear Medicine and Medical Imaging
    Identifiers
    urn:nbn:se:liu:diva-122176 (URN)10.1016/j.heares.2015.12.005 (DOI)000386417900016 ()
    Available from: 2015-10-23 Created: 2015-10-23 Last updated: 2017-12-01Bibliographically approved
    2. Micro CT-scanning of the mastoid. Micro-channels supporting a high vascular supply of the mastoid mucosa and its role in pressure regulation
    Open this publication in new window or tab >>Micro CT-scanning of the mastoid. Micro-channels supporting a high vascular supply of the mastoid mucosa and its role in pressure regulation
    Show others...
    2013 (English)Conference paper, Oral presentation only (Other academic)
    National Category
    Otorhinolaryngology Radiology, Nuclear Medicine and Medical Imaging Medical Image Processing
    Identifiers
    urn:nbn:se:liu:diva-101199 (URN)
    Conference
    1st Global Otology Research Forum, 13 Novenber 2013, Antalya, Turkey
    Available from: 2013-11-20 Created: 2013-11-20 Last updated: 2018-09-11
    3. Structural Analysis of Micro-channels in Human Temporal Bone
    Open this publication in new window or tab >>Structural Analysis of Micro-channels in Human Temporal Bone
    2015 (English)In: IEEE 12th International Symposium on Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on, Institute of Electrical and Electronics Engineers (IEEE), 2015, p. 9-12Conference paper, Published paper (Refereed)
    Abstract [en]

    Recently, numerous micro-channels have been discovered in the human temporal bone by micro-CT-scanning. Preliminary structure of these channels has suggested they contain a new separate blood supply for the mucosa of the mastoid air cells, which may have important functional implications. This paper proposes a structural analysis of the microchannels to corroborate this role. A local structure tensor is first estimated. The eigenvalues obtained from the estimated local structure tensor were then used to build probability maps representing planar, tubular, and isotropic tensor types. Each tensor type was assigned a respective RGB color and the full structure tensor was rendered along with the original data. Such structural analysis provides new and relevant information about the micro-channels but also their connections to mastoid air cells. Before carrying a future statistical analysis, a more accurate representation of the micro-channels in terms of local structure tensor analysis using adaptive filtering is needed.

    Place, publisher, year, edition, pages
    Institute of Electrical and Electronics Engineers (IEEE), 2015
    Series
    IEEE International Symposium on Biomedical Imaging, ISSN 1945-7928
    Keywords
    Human temporal bone, mastoid, microchannels, quadrature filters, structure tensor, visualization
    National Category
    Radiology, Nuclear Medicine and Medical Imaging
    Identifiers
    urn:nbn:se:liu:diva-122177 (URN)10.1109/ISBI.2015.7163804 (DOI)000380546000003 ()978-1-4799-2374-8 (ISBN)
    Conference
    IEEE 12th International Symposium on Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on, 16-19 April, New York, USA
    Available from: 2015-10-23 Created: 2015-10-23 Last updated: 2017-05-10Bibliographically approved
  • 136.
    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.

  • 137.
    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.

  • 138.
    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). Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Denmark.
    Gaihede, Michael
    Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Denmark / Department of Clinical Medicine, Aalborg University, Denmark.
    Andersson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    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).
    Structural Analysis of Micro-channels in Human Temporal Bone2015In: IEEE 12th International Symposium on Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on, Institute of Electrical and Electronics Engineers (IEEE), 2015, p. 9-12Conference paper (Refereed)
    Abstract [en]

    Recently, numerous micro-channels have been discovered in the human temporal bone by micro-CT-scanning. Preliminary structure of these channels has suggested they contain a new separate blood supply for the mucosa of the mastoid air cells, which may have important functional implications. This paper proposes a structural analysis of the microchannels to corroborate this role. A local structure tensor is first estimated. The eigenvalues obtained from the estimated local structure tensor were then used to build probability maps representing planar, tubular, and isotropic tensor types. Each tensor type was assigned a respective RGB color and the full structure tensor was rendered along with the original data. Such structural analysis provides new and relevant information about the micro-channels but also their connections to mastoid air cells. Before carrying a future statistical analysis, a more accurate representation of the micro-channels in terms of local structure tensor analysis using adaptive filtering is needed.

  • 139.
    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.

  • 140.
    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). Department of Otolaryngology, Head and 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).
    Andersson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Pawels, Elin
    Centre for X-ray Tomography, Department of Physics and Astronomy, University of Ghent, Belgium.
    Borga, Magnus
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Gaihede, Michael
    Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Denmark / Department of Clinical Medicine, Aalborg University, Denmark.
    Determination of the mastoid surface area and volume based on micro-CT scanning of human temporal bone: Geometrical parameters dependence on scanning resolutions2016In: Hearing Research, ISSN 0378-5955, E-ISSN 1878-5891, Vol. 340, p. 127-134Article in journal (Other academic)
    Abstract [en]

    The mastoid air cell system (MACS) with its large complex of interconnected air cells reflects an enhanced surface area (SA) relative to its volume (V), which may indicate that the MACS is adapted to gas exchange and has a potential role in middle ear pressure regulation. Thus, these geometric parameters of the MACS have been studied by high resolution clinical CT scanning. However, the resolution of these scans is limited to a voxel size of around 0.6 mm in all dimensions, and so, the geometrical parameters are also limited. Small air cells may appear below the resolution and cannot be detected. Such air cells may contribute to a much higher SA than the V, and thus, also the SA/V ratio. More accurate parameters are important for analysis of the function of the MACS including physiological modeling.

    Our aim was to determine the SA, V, and SA/V ratio in MACS in human temporal bones at highest resolution by using micro-CT-scanning. Further, the influence of the resolution on these parameters was investigated by downsampling the data. Eight normally aerated temporal bones were scanned at the highest possible resolution (30-60 μm). The SA was determined using a triangular mesh fitted onto the segmented MACS. The V was determined by summing all the voxels containing air. Downsampling of the original data was applied four times by a factor of 2.

    The mean SA was 194 cm2, the mean V was 9 cm3, and the mean SA/V amounted to 22 cm-1. Decreasing the resolution resulted in a non-linear decrement of SA and SA/V, whereas V was mainly independent of the resolution.

    The current study found significantly higher SA and SA/V compared with previous studies using clinical CT scanning at lower resolutions. These findings indicate a separate role of the MACS compared with the tympanum, and the results are important for a more accurate modeling of the middle ear physiology.

  • 141.
    Dahlqvist Leinhard, Olof
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences. Linköping University, Faculty of Health Sciences.
    Johansson, Andreas
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Rydell, Joakim
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Kihlberg, Johan
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Faculty of Health Sciences. Linköping University, Department of Medical and Health Sciences. Östergötlands Läns Landsting, Center for Diagnostics, Department of Radiology in Linköping.
    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 Medical Imaging, Department of Radiology in Linköping.
    Nyström, Fredrik H.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Medical and Health Sciences. Linköping University, Faculty of Health Sciences.
    Lundberg, Peter
    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 Medical Imaging, Department of Radiology in Linköping.
    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.
    Quantification of abdominal fat accumulation during hyperalimentation using MRI2009In: Proceedings of the ISMRM Annual Meeting (ISMRM'09), 2009, Berkeley, CA, USA: International Society for Magnetic Resonance in Medicine , 2009, p. 206-Conference paper (Other academic)
    Abstract [en]

    There is an increasing demand for imaging methods that can be used for automatic, accurate and quantitative determination of the amounts of abdominal fat. Such methods are important as they will allow the evaluation of some of the risk factors underlying the ’metabolic syndrome’. The metabolic syndrome is becoming common in large parts of the world, and it appears that a dominant risk factor for developing this syndrome is abdominal obesity. Subjects that are afflicted with the metabolic syndrome are exposed to a high risk for developing a large range of diseases such as type 2 diabetes, cardiac failure, and stroke. The aim of this work

  • 142.
    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.

  • 143.
    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.

  • 144.
    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)
  • 145.
    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)
  • 146.
    Dahlström, Örjan
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Babic, Ankica
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Antonsson, Johan
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Lönn, Urban
    Uppsala Universitet.
    Ahn, Henrik Casimir
    Linköping University, Department of Medicine and Care, Thoracic Surgery. Linköping University, Faculty of Health Sciences. Östergötlands Läns Landsting, Heart Centre, Department of Thoracic and Vascular Surgery.
    Clustering as a data mining method in a Web-based system for thoracic surgery2001In: Journal of the Medical Informatics Association. Symposium Supplement, Washington: Hanley&Belfus , 2001, p. 888-Conference paper (Refereed)
    Abstract [en]

    Cluster analysis is one way of data mining from large amounts of information. Being able to perform series of analyses, varying clinical criteria and requests, expected results of the clustering might be truly rewarding. Instead of having a few hypotheses prepared and tested, medical experts can be surprised by obtaining a set of hypotheses to further validate and work on.

    Internet technologies enable a substantial flexibility that can be taken advantage of when implementing a Web-based tool. Division of Medical Informatics together with Linkoping Heart Center of the Linkoping University is developing procedures for multivariate clustering within the Web-based AssistMe1 system.

  • 147.
    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.

  • 148.
    Dentler, Kathrin
    et al.
    Vrije University of Amsterdam, Netherlands; University of Amsterdam, Netherlands.
    Cornet, Ronald
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. University of Amsterdam, Netherlands.
    Intra-axiom redundancies in SNOMED CT2015In: Artificial Intelligence in Medicine, ISSN 0933-3657, E-ISSN 1873-2860, Vol. 65, no 1, p. 29-34Article in journal (Refereed)
    Abstract [en]

    Objective: Intra-axiom redundancies are elements of concept definitions that are redundant as they are entailed by other elements of the concept definition. While such redundancies are harmless from a logical point of view, they make concept definitions hard to maintain, and they might lead to content-related problems when concepts evolve. The objective of this study is to develop a fully automated method to detect intra-axiom redundancies in OWL 2 EL and apply it to SNOMED Clinical Terms (SNOMED CT). Materials and methods: We developed a software program in which we implemented, adapted and extended readily existing rules for redundancy elimination. With this, we analysed occurence of redundancy in 11 releases of SNOMED CT(January 2009 to January 2014). We used the ELK reasoner to classify SNOMED CT, and Pellet for explanation of equivalence. We analysed the completeness and soundness of the results by an in-depth examination of the identified redundant elements in the July 2012 release of SNOMED CT. To determine if concepts with redundant elements lead to maintenance issues, we analysed a small sample of solved redundancies. Results: Analyses showed that the amount of redundantly defined concepts in SNOMED CT is consistently around 35,000. In the July 2012 version of SNOMED CT, 35,010(12%) of the 296,433 concepts contained redundant elements in their definitions. The results of applying our method are sound and complete with respect to our evaluation. Analysis of solved redundancies suggests that redundancies in concept definitions lead to inadequate maintenance of SNOMED CT. Conclusions: Our analysis revealed that redundant elements are continuously introduced and removed, and that redundant elements may be overlooked when concept definitions are corrected. Applying our redundancy detection method to remove intra-axiom redundancies from the stated form of SNOMED CT and to point knowledge modellers to newly introduced redundancies can support creating and maintaining a redundancy-free version of SNOMED CT. (C) 2014 Elsevier B.V. All rights reserved.

  • 149.
    Dentler, Kathrin
    et al.
    Vrije University of Amsterdam, Netherlands University of Amsterdam, Netherlands .
    Numans, Mattijs E.
    University of Medical Centre Utrecht, Netherlands Vrije University of Amsterdam, Netherlands .
    ten Teije, Annette
    Vrije University of Amsterdam, Netherlands .
    Cornet, Ronald
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. University of Amsterdam, Netherlands.
    de Keizer, Nicolette F.
    University of Amsterdam, Netherlands .
    Formalization and computation of quality measures based on electronic medical records2014In: JAMIA Journal of the American Medical Informatics Association, ISSN 1067-5027, E-ISSN 1527-974X, Vol. 21, no 2, p. 285-291Article in journal (Refereed)
    Abstract [en]

    Objective Ambiguous definitions of quality measures in natural language impede their automated computability and also the reproducibility, validity, timeliness, traceability, comparability, and interpretability of computed results. Therefore, quality measures should be formalized before their release. We have previously developed and successfully applied a method for clinical indicator formalization (CLIF). The objective of our present study is to test whether CLIF is generalizablethat is, applicable to a large set of heterogeneous measures of different types and from various domains. Materials and methods We formalized the entire set of 159 Dutch quality measures for general practice, which contains structure, process, and outcome measures and covers seven domains. We relied on a web-based tool to facilitate the application of our method. Subsequently, we computed the measures on the basis of a large database of real patient data. Results Our CLIF method enabled us to fully formalize 100% of the measures. Owing to missing functionality, the accompanying tool could support full formalization of only 86% of the quality measures into Structured Query Language (SQL) queries. The remaining 14% of the measures required manual application of our CLIF method by directly translating the respective criteria into SQL. The results obtained by computing the measures show a strong correlation with results computed independently by two other parties. Conclusions The CLIF method covers all quality measures after having been extended by an additional step. Our web tool requires further refinement for CLIF to be applied completely automatically. We therefore conclude that CLIF is sufficiently generalizable to be able to formalize the entire set of Dutch quality measures for general practice.

  • 150.
    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.

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