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  • 1.
    Abedan Kondori, Farid
    et al.
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Yousefi, Shahrouz
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Li, Haibo
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Sonning, Samuel
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Sonning, Sabina
    3D Head Pose Estimation Using the Kinect2011Conference paper (Refereed)
    Abstract [en]

    Head pose estimation plays an essential role for bridging the information gap between humans and computers. Conventional head pose estimation methods are mostly done in images captured by cameras. However accurate and robust pose estimation is often problematic. In this paper we present an algorithm for recovering the six degrees of freedom (DOF) of motion of a head from a sequence of range images taken by the Microsoft Kinectfor Xbox 360. The proposed algorithm utilizes a least-squares minimization of the difference between themeasured rate of change of depth at a point and the rate predicted by the depth rate constraint equation. We segment the human head from its surroundings and background, and then we estimate the head motion. Our system has the capability to recover the six DOF of the head motion of multiple people in one image. Theproposed system is evaluated in our lab and presents superior results.

  • 2.
    Abedan Kondori, Farid
    et al.
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Yousefi, Shahrouz
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Liu, Li
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Active human gesture capture for diagnosing and treating movement disorders2013Conference paper (Other academic)
    Abstract [en]

    Movement disorders prevent many people fromenjoying their daily lives. As with other diseases, diagnosisand analysis are key issues in treating such disorders.Computer vision-based motion capture systems are helpfultools for accomplishing this task. However Classical motiontracking systems suffer from several limitations. First theyare not cost effective. Second these systems cannot detectminute motions accurately. Finally they are spatially limitedto the lab environment where the system is installed. In thisproject, we propose an innovative solution to solve the abovementionedissues. Mounting the camera on human body, webuild a convenient, low cost motion capture system that canbe used by the patient in daily-life activities. We refer tothis system as active motion capture, which is not confinedto the lab environment. Real-time experiments in our labrevealed the robustness and accuracy of the system.

  • 3.
    Adjeiwaah, Mary
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Quality assurance for magnetic resonance imaging (MRI) in radiotherapy2017Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Magnetic resonance imaging (MRI) utilizes the magnetic properties of tissues to generate image-forming signals. MRI has exquisite soft-tissue contrast and since tumors are mainly soft-tissues, it offers improved delineation of the target volume and nearby organs at risk. The proposed Magnetic Resonance-only Radiotherapy (MR-only RT) work flow allows for the use of MRI as the sole imaging modality in the radiotherapy (RT) treatment planning of cancer. There are, however, issues with geometric distortions inherent with MR image acquisition processes. These distortions result from imperfections in the main magnetic field, nonlinear gradients, as well as field disturbances introduced by the imaged object. In this thesis, we quantified the effect of system related and patient-induced susceptibility geometric distortions on dose distributions for prostate as well as head and neck cancers. Methods to mitigate these distortions were also studied.

    In Study I, mean worst system related residual distortions of 3.19, 2.52 and 2.08 mm at bandwidths (BW) of 122, 244 and 488 Hz/pixel up to a radial distance of 25 cm from a 3T PET/MR scanner was measured with a large field of view (FoV) phantom. Subsequently, we estimated maximum shifts of 5.8, 2.9 and 1.5 mm due to patient-induced susceptibility distortions. VMAT-optimized treatment plans initially performed on distorted CT (dCT) images and recalculated on real CT datasets resulted in a dose difference of less than 0.5%.

     The magnetic susceptibility differences at tissue-metallic,-air and -bone interfaces result in local B0 magnetic field inhomogeneities. The distortion shifts caused by these field inhomogeneities can be reduced by shimming.  Study II aimed to investigate the use of shimming to improve the homogeneity of local  B0 magnetic field which will be beneficial for radiotherapy applications. A shimming simulation based on spherical harmonics modeling was developed. The spinal cord, an organ at risk is surrounded by bone and in close proximity to the lungs may have high susceptibility differences. In this region, mean pixel shifts caused by local B0 field inhomogeneities were reduced from 3.47±1.22 mm to 1.35±0.44 mm and 0.99±0.30 mm using first and second order shimming respectively. This was for a bandwidth of 122 Hz/pixel and an in-plane voxel size of 1×1 mm2.  Also examined in Study II as in Study I was the dosimetric effect of geometric distortions on 21 Head and Neck cancer treatment plans. The dose difference in D50 at the PTV between distorted CT and real CT plans was less than 1.0%.

    In conclusion, the effect of MR geometric distortions on dose plans was small. Generally, we found patient-induced susceptibility distortions were larger compared with residual system distortions at all delineated structures except the external contour. This information will be relevant when setting margins for treatment volumes and organs at risk.  

    The current practice of characterizing MR geometric distortions utilizing spatial accuracy phantoms alone may not be enough for an MR-only radiotherapy workflow. Therefore, measures to mitigate patient-induced susceptibility effects in clinical practice such as patient-specific correction algorithms are needed to complement existing distortion reduction methods such as high acquisition bandwidth and shimming.

  • 4. Agogo, George O.
    et al.
    van der Voet, Hilko
    van 't Veer, Pieter
    Ferrari, Pietro
    Muller, David C.
    Sanchez-Cantalejo, Emilio
    Bamia, Christina
    Braaten, Tonje
    Knuppel, Sven
    Johansson, Ingegerd
    Umeå University, Faculty of Medicine, Department of Odontology.
    van Eeuwijk, Fred A.
    Boshuizen, Hendriek C.
    A method for sensitivity analysis to assess the effects of measurement error in multiple exposure variables using external validation data2016In: BMC Medical Research Methodology, ISSN 1471-2288, E-ISSN 1471-2288, Vol. 16, article id 139Article in journal (Refereed)
    Abstract [en]

    Background: Measurement error in self-reported dietary intakes is known to bias the association between dietary intake and a health outcome of interest such as risk of a disease. The association can be distorted further by mismeasured confounders, leading to invalid results and conclusions. It is, however, difficult to adjust for the bias in the association when there is no internal validation data. Methods: We proposed a method to adjust for the bias in the diet-disease association (hereafter, association), due to measurement error in dietary intake and a mismeasured confounder, when there is no internal validation data. The method combines prior information on the validity of the self-report instrument with the observed data to adjust for the bias in the association. We compared the proposed method with the method that ignores the confounder effect, and with the method that ignores measurement errors completely. We assessed the sensitivity of the estimates to various magnitudes of measurement error, error correlations and uncertainty in the literature-reported validation data. We applied the methods to fruits and vegetables (FV) intakes, cigarette smoking (confounder) and all-cause mortality data from the European Prospective Investigation into Cancer and Nutrition study. Results: Using the proposed method resulted in about four times increase in the strength of association between FV intake and mortality. For weakly correlated errors, measurement error in the confounder minimally affected the hazard ratio estimate for FV intake. The effect was more pronounced for strong error correlations. Conclusions: The proposed method permits sensitivity analysis on measurement error structures and accounts for uncertainties in the reported validity coefficients. The method is useful in assessing the direction and quantifying the magnitude of bias in the association due to measurement errors in the confounders.

  • 5.
    Ahlgren, Ulf
    et al.
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Kostromina, Elena
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Imaging the pancreatic beta cell: chapter 132011In: Type 1 diabetes: pathogenesis, genetics and immunotherapy / [ed] David Wagner, InTech, 2011Chapter in book (Refereed)
    Abstract [en]

    This book is a compilation of reviews about the pathogenesis of Type 1 Diabetes. T1D is a classic autoimmune disease. Genetic factors are clearly determinant but cannot explain the rapid, even overwhelming expanse of this disease. Understanding etiology and pathogenesis of this disease is essential. A number of experts in the field have covered a range of topics for consideration that are applicable to researcher and clinician alike. This book provides apt descriptions of cutting edge technologies and applications in the ever going search for treatments and cure for diabetes. Areas including T cell development, innate immune responses, imaging of pancreata, potential viral initiators, etc. are considered.

  • 6.
    Al Khodor, Rami
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Rörelseanalyssystem2014Independent thesis Basic level (professional degree), 180 HE creditsStudent thesis
    Abstract [sv]

    Idag ses ett ökat intresse för användandet av rörelseanalys inom olika sammanhang t.ex. övervakning, dataspel och diagnostisk undersökning av personers rörelsemönster med mera. Optisk rörelseanalys är den teknik som finns mest idag, men de systemen är dyra och saknar lämplig mjukvara för klinisk användning.

    En forskargrupp vid centrum för medicinsk teknik och strålningsfysik (CMTS) forskning och utvecklings avdelning (MT-FoU) vid Norrlands universitetssjukhus har sedan 2007 jobbat med en produktidé som bygger på att skapa ett nytt mobilt system för rörelseanalys som kan användas i medicinska undersökningar. Ett Arduino pro mini kort samt ett 9-axligt prototypkort som består av MPU-6000 och en magnetometer HMC5883L är anskaffat för att tillverka ett system i detta syfte.

    Syftet med projektet har varit att skapa ett verktyg som kan samla in rörelsemönster för att sedan presentera resultatet i ett diagram. Systemet skulle kunna samla in data från en sensor som inkluderar en 3D-accelerometer ett 3D-gyroskop och en 3D magnetometer för att därefter skicka det vidare till en dator där mätdata presenteras visuellt och sparas undan i en textfil.

    En viktig detalj att ta hänsyn till vid konstruktionen av det nya systemet var att konstruktionen gjordes med hjälp av billiga standardkomponenter och kretskort. Projektet har genomförts och några testmätningar har gjorts. Ett resultat sparades undan i en textfil och ett diagram har tagits fram som beskriver ett lårs rörelsemönster vid normal gång.

  • 7.
    Albano, Amanda
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Exploratory statistical study of long-term variability in echocardiographic indices (echocardiovariability) in healthy and diseased1987Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Heart rate variability, HRV, has been well researched for some decades. The oscillations of the heart rate is studied over a time period of some minutes up to 24 hours, it is measured with electrocardiography, ECG. From this one has concluded that the heart rate signal oscillates in accordance with the respiration, the resistance in the vessels etc.

    The most frequently used examination method of the heart is done with ultrasound, called echocardiography. One interesting variable at a time is measured and it is measured for a single heartbeat. With inspiration ofthe HRV studies this project focuses on some of the variables measured with ultrasound but over time andsimultaneously. The variables of interest are the myocardial motion and the blood flow in the left part ofthe heart, they are measured over two minutes. To complement these variables the well known variables HRand Resp are measured with ECG and added to the analysis.

    The methods used for analysing the variables are first of all descriptive statistics like mean and standard deviation. Secondly spectral analysis is performed to investigate in which frequencies the variables oscillates. Through coherence this is compared with the spectrum for HR where the three peaks have known origin. Finally principal component analysis, PCA, is performed as a method to compare all variables at the same time.

    The analyses are performed on seven measurements from five (5) healthy persons and five measurementsfrom four (4) patients with the disease FAP (“Skelleftesjukan”). The variables are investigated and described for the healthy persons first, then the healthy persons and patients are compared.

    The result from the study shows that most of the echo-variables oscillate in accordance with the respirationand the heart rate. For a healthy person the oscillations are within normal values and the relative deviation isaround 10%. The patients with FAP are most affected in the variables connected to the myocardium apartfrom HR, which is known since before.

    The coherence between the echo-variables and HR is low in one of VLF, very low frequency, or LF, lowfrequency, region and high in the other. In HF, high frequency, region the coherence is high for all variables.

    Finally the PCA was conducted on measurements from all healthy persons as one data set, from one ofthe healthy persons and from one of the patients with FAP. The analysis showed that for healthy personsrespiration is the process causing most variation and all of the echo-variables have a correlation to therespiration. For a patient with FAP the respiration is not as salient. A PCA over blocks of data at different time points however show that the signals are not oscillating in the same way multivariately over the wholetime series.

  • 8.
    Ambarki, Khalid
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Lindqvist, Tomas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Wåhlin, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Petterson, E
    Warntjes, JBM
    Birgander, Richard
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology.
    Malm, Jan
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Neuroscience.
    Eklund, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Evaluation of automatic measurement of the intracranial volume based on quantitative MR imaging2012In: American Journal of Neuroradiology, ISSN 0195-6108, E-ISSN 1936-959X, Vol. 33, no 10, p. 1951-1956Article in journal (Refereed)
    Abstract [en]

    BACKGROUND AND PURPOSE: Brain size is commonly described in relation to ICV, whereby accurate assessment of this quantity is fundamental. Recently, an optimized MR sequence (QRAPMASTER) was developed for simultaneous quantification of T1, T2, and proton density. ICV can be measured automatically within minutes from QRAPMASTER outputs and a dedicated software, SyMRI. Automatic estimations of ICV were evaluated against the manual segmentation.

    MATERIALS AND METHODS: In 19 healthy subjects, manual segmentation of ICV was performed by 2 neuroradiologists (Obs1, Obs2) by using QBrain software and conventional T2-weighted images. The automatic segmentation from the QRAPMASTER output was performed by using SyMRI. Manual corrections of the automatic segmentation were performed (corrected-automatic) by Obs1 and Obs2, who were blinded from each other. Finally, the repeatability of the automatic method was evaluated in 6 additional healthy subjects, each having 6 repeated QRAPMASTER scans. The time required to measure ICV was recorded.

    RESULTS: No significant difference was found between reference and automatic (and corrected-automatic) ICV (P > .25). The mean difference between the reference and automatic measurement was -4.84 ± 19.57 mL (or 0.31 ± 1.35%). Mean differences between the reference and the corrected-automatic measurements were -0.47 ± 17.95 mL (-0.01 ± 1.24%) and -1.26 ± 17.68 mL (-0.06 ± 1.22%) for Obs1 and Obs2, respectively. The repeatability errors of the automatic and the corrected-automatic method were <1%. The automatic method required 1 minute 11 seconds (SD = 12 seconds) of processing. Adding manual corrections required another 1 minute 32 seconds (SD = 38 seconds).

    CONCLUSIONS: Automatic and corrected-automatic quantification of ICV showed good agreement with the reference method. SyMRI software provided a fast and reproducible measure of ICV.

  • 9.
    Andersson, Britt
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Svängande sensorer hittar prostatacancer2010In: medtechinfo.comArticle in journal (Other (popular science, discussion, etc.))
  • 10. Andersson, Martin
    et al.
    Mattsson, Soren
    Johansson, Lennart
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Leide-Svegborn, Sigrid
    A biokinetic and dosimetric model for ionic indium in humans2017In: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560, Vol. 62, no 16, p. 6397-6407Article in journal (Refereed)
    Abstract [en]

    This paper reviews biokinetic data for ionic indium, and proposes a biokinetic model for systemic indium in adult humans. The development of parameter values focuses on human data and indium in the form of ionic indium(III), as indium chloride and indium arsenide. The model presented for systemic indium is defined by five different pools: plasma, bone marrow, liver, kidneys and other soft tissues. The model is based on two subsystems: one corresponding to indium bound to transferrin and one where indium is transported back to the plasma, binds to red blood cell transferrin and is then excreted through the kidneys to the urinary bladder. Absorbed doses to several organs and the effective dose are calculated for In-111- and In-113m-ions. The proposed biokinetic model is compared with previously published biokinetic indium models published by the ICRP. The absorbed doses are calculated using the ICRP/ICRU adult reference phantoms and the effective dose is estimated according to ICRP Publication 103. The effective doses for In-111 and In-113m are 0.25 mSv MBq(-1) and 0.013 mSv MBq(-1) respectively. The updated biokinetic and dosimetric models presented in this paper take into account human data and new animal data, which represent more detailed and presumably more accurate dosimetric data than that underlying previous models for indium.

  • 11.
    Andersson, Nina
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Cerebrospinal fluid infusion methods: development and validation on patients with idiopathic normal pressure hydrocephalus2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cerebrospinal fluid (CSF) infusion tests can be used to estimate the dynamic properties of the CSF system. Idiopathic normal pressure hydrocephalus (INPH) is a syndrome signified by a disturbance to the CSF system, where the cause is unknown and the diagnosis is difficult to determine. As an aid in identifying patients with INPH who will improve after shunt surgery, infusion tests are commonly used to determine the outflow conductance (Cout), or outflow resistance (Rout=1/Cout), of the CSF system. The tests are also used to determine shunt function in vivo. The general aim of this thesis was to develop and validate CSF infusion methods, to investigate the dynamics of the CSF system. The methods should be applicable to patients with INPH, to aid in the quest to further improve the diagnosis and management of this syndrome.

    An existing mathematical model describing the dynamics of the CSF system was further developed. The characteristics of the model were verified and the effect of expanding intracranial air on the intracranial pressure (ICP) was simulated. The simulations supported the recommendation to maintain sea-level pressure during air ambulance transportation of patients with suspected intracranial air.

    A recently developed infusion apparatus was evaluated, on an experimental model as well as on a patient material. The repetitiveness in estimating Cout was found to be good. A statistically significant difference was found between the repeated Cout estimations in the patient group, indicating that there might have been a small physiological change introduced during the infusion test. A parameter, ∆Cout, was proposed and evaluated. It proved to reflect the reliability of individual Cout investigations in a clinically useful way, as well as to provide easily interpreted information.

    An adaptive algorithm for assessment of Cout was developed and evaluated on a patient group. The new algorithm was shown to reduce the investigation time, from 60 minutes, by 14.3 ± 5.9 minutes (mean ± SD), p<0.01, without reducing the reliability of the estimated Cout below clinically relevant levels.

    The relationship between ICP and CSF outflow was studied in a group of patients investigated for INPH. It was found that in the range of moderate increase from baseline pressure, the assumption of a pressure independent Rout was confirmed (p=0.5). However, at larger pressure increments, the relationship had a non-linear tendency (p<0.05). This indicates that the traditional view of a pressure independent Rout might have to be questioned in the region where ICP exceeds baseline pressure too much.

    Infusion tests can be performed in different ways, where three main categories may be distinguished. The bolus infusion method was compared to the constant pressure and constant flow infusion methods, on an experimental model as well as on a patient material. When physiological pressure fluctuations were added to the model, significant differences were found in the determination of Cout in the range of clinical importance, i.e. low Cout (p<0.05). The finding was supported by the patient investigations, the difference was however not significant.

    With the application of the new methods developed in this thesis, and the increased knowledge concerning relationships between CSF dynamic parameters, the CSF infusion test was further improved with the ability to increase measurement reliability in a reduced time. This constitutes a good basis to perform a large multi-centre study with the main goal to determine the predictive value of the parameter Cout.

  • 12.
    Arnlund, Caroline
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Utveckling av sensor för mätning av hjärtaktivitet2014Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Motion analysis is a necessary tool when it comes to evaluation, monitoring and diagnosis of all the diseases that affect the human musculoskeletal system. There are only a few clinical walking laboratories in Sweden, where the patients can receive a more detailed and objective evaluation of their walking patterns. The problem with these laboratories is that they are relatively expensive and resource-demanding.

    The department of research and development at NUS has initiated a research project where AnyMo, a mobile system for measuring of moving patterns, was produced. The aim of this thesis was to further develop the existing system to simultaneously measure the electrical activity of the heart (ECG).

    The parts that were constructed during this project was an ECG sensor and a Master Unit, coupled to an existing motion sensor (part of the AnyMo system). The information that was collected from these sensors was stored locally in a memory on the system’s Master Unit.

    The finished product was tested and evaluated on a stationary bike at different pace and heart rate.

  • 13. Asan, Noor Badariah
    et al.
    Noreland, Daniel
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Hassan, Emadeldeen
    Umeå University, Faculty of Science and Technology, Department of Computing Science. Department of Electronics and Electrical Communications, Menoufia University, Menouf, Egypt.
    Shah, Syaiful Redzwan Mohd
    Rydberg, Anders
    Blokhuis, Taco J.
    Carlsson, Per-Ola
    Voigt, Thiemo
    Augustine, Robin
    Intra-body microwave communication through adipose tissue2017In: Healthcare technology letters, E-ISSN 2053-3713, Vol. 4, no 4, p. 115-121Article in journal (Refereed)
    Abstract [en]

    The human body can act as a medium for the transmission of electromagnetic waves in the wireless body sensor networks context. However, there are transmission losses in biological tissues due to the presence of water and salts. This Letter focuses on lateral intra-body microwave communication through different biological tissue layers and demonstrates the effect of the tissue thicknesses by comparing signal coupling in the channel. For this work, the authors utilise the R-band frequencies since it overlaps the industrial, scientific and medical radio (ISM) band. The channel model in human tissues is proposed based on electromagnetic simulations, validated using equivalent phantom and ex-vivo measurements. The phantom and ex-vivo measurements are compared with simulation modelling. The results show that electromagnetic communication is feasible in the adipose tissue layer with a low attenuation of approximate to 2 dB per 20 mm for phantom measurements and 4 dB per 20 mm for ex-vivo measurements at 2 GHz. Since the dielectric losses of human adipose tissues are almost half of ex-vivo tissue, an attenuation of around 3 dB per 20 mm is expected. The results show that human adipose tissue can be used as an intra-body communication channel.

  • 14. Asan, Noor Badariah
    et al.
    Redzwan, Syaiful
    Rydberg, Anders
    Augustine, Robin
    Noreland, Daniel
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Hassan, Emadeldeen
    Umeå University, Faculty of Science and Technology, Department of Computing Science. Department of Electronics and Electrical Communications, Menoufia University, Menouf, Egypt.
    Voigt, Thiemo
    Human Fat Tissue: A Microwave Communication Channel2017In: 2017 First IEEE MTT-S International Microwave Bio Conference (IMBIOC), IEEE, 2017Conference paper (Refereed)
    Abstract [en]

    In this paper, we present an approach for communication through human body tissue in the R-band frequency range. This study examines the ranges of microwave frequencies suitable for intra-body communication. The human body tissues are characterized with respect to their transmission properties using simulation modeling and phantom measurements. The variations in signal coupling with respect to different tissue thicknesses are studied. The simulation and phantom measurement results show that electromagnetic communication in the fat layer is viable with attenuation of approximately 2 dB per 20 mm.

  • 15.
    Asplund, Raquel
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Evaluation of a cloud-based image analysis and image display system for medical images2015Independent thesis Basic level (university diploma), 180 HE creditsStudent thesis
  • 16.
    Axelsson, Jan
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Imlook4d: introducing an extendable research 4d analysis software2014In: XII Turku PET Symposium, 24-27 May 2014, Turku, Finland: the symposium of Nordic Association for Clinical Physics (NACP), 2014, p. 63-63Conference paper (Other academic)
    Abstract [en]

    Imlook4d (http://www.dicom-port.com) is a free Matlab based graphical user interface (GUI) tool useful for static, dynamic and gated PET studies.  It supports reading and writing DICOM, Nifti, Analyze, ECAT.  The DICOM reader is orders of magnitude faster than the Matlab imaging toolbox.  Imlook4d requires no additional Matlab toolboxes.

    The main benefit with imlook4d is that it is easily extendable with scripts, accessing exported variables such as the image matrix (4D) and a region-of-interest (ROI) matrix.  Scripts are available via a menu in the imlook4d GUI, and can be used to manipulate the image-matrix and ROI data.  There is also a menu option to export and import these variables to the Matlab workspace for interactive manipulation, useful for one-off fixes or for script development.  There are presently about 30 scripts in categories such as ROI, Matrix, Header info etc.  There is also direct export to ImageJ [1] and import back from ImageJ, thus giving access to all tools available within ImageJ.

    Imlook4d has a built in volume-of-interest editor, with a brush tool for quick interactive ROI delineation, and via scripts, different ways of thresholding ROIs from parts of the image.  Time activity data is saved to a tab-delimited text file.

    The principal-component (PC) based Hotelling filter is an integrated part of the program, which allows for interactive noise reduction without loss of quantitation [2].  A typical work flow for a dynamic data set is to turn on the filter for ROI delineation, and then there is the choice of turning it off for export of time-activity data.  Also the PC images can be used to draw ROIs on, which under some circumstances gives enhanced contrast.

    Calculation of parametric pharmacokinetic modelling images can be performed interactively, calculated slice by slice as the user scrolls through the volume.  Reference models for Patlak, Logan and Averaged Simple Flow Model [3]  applied on 15O-water are implemented, and it is relatively easy to implement other kinetic models.  Similarly, scripts have been developed for regional Patlak and Logan models on ROI data.

    [1] Rasband, WS, ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA, http://imagej.nih.gov/ij/, 1997-2014

    [2] Axelsson J, Sörensen J, The 2D Hotelling filter - a quantitative noise-reducing principal-component filter for dynamic PET data, with applications in patient dose reduction. BMC Med Phys. 2013 Apr 10;13:1. doi: 10.1186/1756-6649-13-1.

    [3] Yoshida, K, Mullani, N and Gould KL, Coronary Flow and Flow Reserve by PET Simplified for Clinical Applications Using Rubidium-82 or Nitrogen-13-Ammonia, J Nucl Med 1996; 37:1701-1712

    Figure 1.  The imlook4d GUI with the user SCRIPTS menu selected.  The group of ROI scripts was further selected.  In the underlying image, a rough ROI is created.  

  • 17.
    Axelsson, Jan
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Sörensen, Jens
    PET-center, Department of Radiology, Oncology and Radiation Sciences, Uppsala University, Uppsala, Sweden.
    The 2D Hotelling filter: a quantitativenoise-reducing principal-component filter fordynamic PET data, with applications in patientdose reduction2013In: BMC Medical Physics, ISSN 1756-6649, Vol. 13, no 1Article in journal (Refereed)
    Abstract [en]

    Background: In this paper we apply the principal-component analysis filter (Hotelling filter) to reduce noise fromdynamic positron-emission tomography (PET) patient data, for a number of different radio-tracer molecules. Wefurthermore show how preprocessing images with this filter improves parametric images created from suchdynamic sequence.We use zero-mean unit variance normalization, prior to performing a Hotelling filter on the slices of a dynamictime-series. The Scree-plot technique was used to determine which principal components to be rejected in thefilter process. This filter was applied to [11C]-acetate on heart and head-neck tumors, [18F]-FDG on liver tumors andbrain, and [11C]-Raclopride on brain. Simulations of blood and tissue regions with noise properties matched to realPET data, was used to analyze how quantitation and resolution is affected by the Hotelling filter. Summing varyingparts of a 90-frame [18F]-FDG brain scan, we created 9-frame dynamic scans with image statistics comparable to 20MBq, 60 MBq and 200 MBq injected activity. Hotelling filter performed on slices (2D) and on volumes (3D) werecompared.Results: The 2D Hotelling filter reduces noise in the tissue uptake drastically, so that it becomes simple to manuallypick out regions-of-interest from noisy data. 2D Hotelling filter introduces less bias than 3D Hotelling filter in focalRaclopride uptake. Simulations show that the Hotelling filter is sensitive to typical blood peak in PET prior to tissueuptake have commenced, introducing a negative bias in early tissue uptake. Quantitation on real dynamic data isreliable. Two examples clearly show that pre-filtering the dynamic sequence with the Hotelling filter prior toPatlak-slope calculations gives clearly improved parametric image quality. We also show that a dramatic dosereduction can be achieved for Patlak slope images without changing image quality or quantitation.Conclusions: The 2D Hotelling-filtering of dynamic PET data is a computer-efficient method that gives visuallyimproved differentiation of different tissues, which we have observed improve manual or automated regionof-interest delineation of dynamic data. Parametric Patlak images on Hotelling-filtered data display improved clarity,compared to non-filtered Patlak slope images without measurable loss of quantitation, and allow a dramaticdecrease in patient injected dose.

  • 18. Badariah Asan, Noor
    et al.
    Hassan, Emadeldeen
    Umeå University, Faculty of Science and Technology, Department of Computing Science. Department of Electronics and Electrical Communications, Menoufia University, Menouf, Egypt.
    Velander, Jacob
    Redzwan Mohd Shah, Syaiful
    Noreland, Daniel
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Blokhuis, Taco J.
    Wadbro, Eddie
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Berggren, Martin
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Voigt, Thiemo
    Augustine, Robin
    Characterization of the Fat Channel for Intra-Body Communication at R-Band Frequencies2018In: Sensors, ISSN 1424-8220, E-ISSN 1424-8220, Vol. 18, no 9, article id 2752Article in journal (Refereed)
    Abstract [en]

    In this paper, we investigate the use of fat tissue as a communication channel between in-body, implanted devices at R-band frequencies (1.7–2.6 GHz). The proposed fat channel is based on an anatomical model of the human body. We propose a novel probe that is optimized to efficiently radiate the R-band frequencies into the fat tissue. We use our probe to evaluate the path loss of the fat channel by studying the channel transmission coefficient over the R-band frequencies. We conduct extensive simulation studies and validate our results by experimentation on phantom and ex-vivo porcine tissue, with good agreement between simulations and experiments. We demonstrate a performance comparison between the fat channel and similar waveguide structures. Our characterization of the fat channel reveals propagation path loss of ∼0.7 dB and ∼1.9 dB per cm for phantom and ex-vivo porcine tissue, respectively. These results demonstrate that fat tissue can be used as a communication channel for high data rate intra-body networks.

  • 19.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Kuljus, Kristi
    Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia.
    Johansson, Adam
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Bolin, David
    Department of Mathematical Sciences, Chalmers and University of Gothenburg, Gothenburg, Sweden.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Prediction of CT images from MR images with hidden Markov and random field models2016In: Proceedings of the 8th International Workshop on Spatio-Temporal Modelling / [ed] A. Iftimi, J. Mateu and F. Montes, 2016, p. 163-163Conference paper (Other academic)
  • 20.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Liu, Xijia
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Garpebring, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Statistical learning in computed tomography image estimation2018In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 45, no 12, p. 5450-5460Article in journal (Refereed)
    Abstract [en]

    Purpose: There is increasing interest in computed tomography (CT) image estimations from magneticresonance (MR) images. The estimated CT images can be utilized for attenuation correction, patientpositioning, and dose planning in diagnostic and radiotherapy workflows. This study aims to introducea novel statistical learning approach for improving CT estimation from MR images and to compare theperformance of our method with the existing model-based CT image estimation methods.

    Methods: The statistical learning approach proposed here consists of two stages. At the trainingstage, prior knowledge about tissue types from CT images was used together with a Gaussian mixturemodel (GMM) to explore CT image estimations from MR images. Since the prior knowledge is notavailable at the prediction stage, a classifier based on RUSBoost algorithm was trained to estimatethe tissue types from MR images. For a new patient, the trained classifier and GMMs were used topredict CT image from MR images. The classifier and GMMs were validated by using voxel-leveltenfold cross-validation and patient-level leave-one-out cross-validation, respectively.

    Results: The proposed approach has outperformance in CT estimation quality in comparison withthe existing model-based methods, especially on bone tissues. Our method improved CT image estimationby 5% and 23% on the whole brain and bone tissues, respectively.

    Conclusions: Evaluation of our method shows that it is a promising method to generate CTimage substitutes for the implementation of fully MR-based radiotherapy and PET/MRI applications

  • 21.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Model-based Estimation of Computed Tomography Images2017Conference paper (Other academic)
  • 22.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Model-based Estimation of Computed Tomography Images2017Manuscript (preprint) (Other academic)
    Abstract [en]

    There is a growing interest to get a fully MR based radiotherapy. The most important development needed is to obtain improved bone tissue estimation. Existing model-based methods have performed poorly on bone tissues. This paper aims to obtainimproved estimation of bone tissues. Skew-Gaussian mixture model (SGMM) isproposed to further investigate CT image estimation from MR images. The estimation quality of the proposed model is evaluated using leave-one-out cross-validation method on real data. In comparison with the existing model-based approaches, the approach utilized in this paper outperforms in estimation of bone tissues, especiallyon dense bone tissues.

  • 23.
    Bayisa, Fekadu
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Zhou, Zhiyong
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Cronie, Ottmar
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Adaptive algorithm for sparse signal recovery2019In: Digital signal processing (Print), ISSN 1051-2004, E-ISSN 1095-4333, Vol. 87, p. 16p. 10-18Article in journal (Refereed)
    Abstract [en]

    The development of compressive sensing in recent years has given much attention to sparse signal recovery. In sparse signal recovery, spike and slab priors are playing a key role in inducing sparsity. The use of such priors, however, results in non-convex and mixed integer programming problems. Most of the existing algorithms to solve non-convex and mixed integer programming problems involve either simplifying assumptions, relaxations or high computational expenses. In this paper, we propose a new adaptive alternating direction method of multipliers (AADMM) algorithm to directly solve the suggested non-convex and mixed integer programming problem. The algorithm is based on the one-to-one mapping property of the support and non-zero element of the signal. At each step of the algorithm, we update the support by either adding an index to it or removing an index from it and use the alternating direction method of multipliers to recover the signal corresponding to the updated support. Moreover, as opposed to the competing “adaptive sparsity matching pursuit” and “alternating direction method of multipliers” methods our algorithm can solve non-convex problems directly. Experiments on synthetic data and real-world images demonstrated that the proposed AADMM algorithm provides superior performance and is computationally cheaper than the recently developed iterative convex refinement (ICR) and adaptive matching pursuit (AMP) algorithms.

  • 24.
    Berglund, Anders
    et al.
    Umeå University, Faculty of Medicine, Department of Odontology.
    Branting-Ekenbäck, C
    Ohlson, M
    En översikt över chairside CAD/CAM-system i Sverige. Garanteras patientsäkerheten genom CE-märkningen av utrustning och material?2013Report (Other academic)
    Abstract [sv]

    Inom odontologin har Computer-Aided Design/Computer-Aided Manufacturing (CAD/CAM) blivit allt vanligare, främst på tandtekniska laboratorier, men tekniken blir också vanligare på tandläkarklinikerna, s.k. chairside CAD/CAM. Chairside CAD/CAM innebär att tandläkaren efter preparationen av en tand framställer tandersättningen i tre steg. I första steget används en intraoral scanner istället för den traditionella avtryckstagningen (Mörmann et al., 2002; Beuer et al., 2008; Hehn, 2001). Man kan även scanna modeller och avtryck, vilket kan vara bra om patienten har svårt att gapa eller har hög salivproduktion, då scannrarna är känsliga för fuktiga miljöer (Kachalia et al., 2010). Det digitala avtrycket överförs till datorn, där uppgifterna bearbetas och en modell av tänderna skapas i 3D. I det andra steget designar tandläkaren tandersättningen på 3D-modellen. Här bestämmer tandläkaren kusphöjd, kontakter approximalt, utsträckning mot preparationsgränsen och utseende på tandersättningen. I det tredje steget fräses tandersättningen fram ur ett keramblock i en fräsmaskin. Ofta målas kronan här för att karaktärisera den och ge den ett mer tandlikt utseende innan den bränns i ugn. Med större möjligheter att själv kunna sköta hela processen fram till färdig tandkonstruktion måste tandläkaren fundera över hur kvaliteten och säkerheten hos de färdiga produkterna kan säkerställas. Färdiga tandtekniska arbeten räknas som specialanpassade medicintekniska produkter och ska inte CE-märkas men de material som ingår i arbetet är oftast CE-märkta. Lag (1993:584) om medicintekniska produkter och Läkemedelsverkets föreskrifter (LVFS 2003:11) om medicintekniska produkter innehåller krav på att medicintekniska produkter som släpps ut på marknaden ska vara lämpliga och säkra för sina användningsområden genom att krav ställs som ska leda till att allvarliga avvikelser, olyckor och tillbud på grund av produkterna så långt som möjligt ska kunna undvikas. Avvikelser inkluderar här både funktionsfel och misstänkta biverkningar. Innan ett tandtekniskt laboratorium får börja leverera tandtekniska arbeten till tandläkare måste ett antal krav vara uppfyllda för att bl.a. säkerställa säkerheten hos dessa produkter för patienterna. Laboratoriet ska vara registrerat hos Läkemedelsverket och vid registreringen måste man intyga att man har en tillverkningsverksamhet som uppfyller de krav för specialanpassade medicintekniska produkter som ställs i LVFS 2003:11. Medicintekniska produkter ska konstrueras och tillverkas på ett sådant sätt att de inte äventyrar patienternas kliniska tillstånd eller säkerhet, användarnas eller i förekommande fall andra personers hälsa och säkerhet, när de används under avsedda förhållanden och för sitt avsedda ändamål. Riskerna med att använda produkterna ska vara acceptabla med tanke på fördelarna för patienten och förenliga med en hög hälso-och säkerhetsnivå. Detta innefattar omfattande krav både på produkt och tillverkningsprocess. Det finns en del oklarheter rörande hur det regelverk som styr framställningen av tandtekniska arbeten tillämpas för arbeten tillverkade med chairside CAD/CAM.

  • 25.
    Björnfot, Cecilia
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Multiband functional magnetic resonance imaging (fMRI) for functional connectivity assessments2018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    During resting state the brain exhibits synchronized activity within all major brain networks. Using blood oxygen level dependent (BOLD) resting state functional magnetic resonance imaging (fMRI) based detection it is possible to quantify the degree of correlation, connectivity, between regions of interest and assess information regarding the integrity of the inter-regional functional integration. A newly available multiband echo planar imaging (EPI) fMRI sequence allows for faster scan times which possibly allows us to better examine large-scale networks and increase the understanding of brain function/dysfunction. This thesis will assess how the newly developed sequence compares to a conventional EPI sequence for detecting resting state connectivity of canonical brain networks. The data acquisitions were made on a 3 Tesla scanner using a 32 channel head coil. The hypothesis was that the multiband sequence would produce a better result since it has faster sampling rate, thus more data points in its time-series to support the statistical analyses.

    Using Pearson’s linear correlation between the average time-series (approximately 12 minutes long) within a seed-region and all voxels contained in the image volume, correlation maps where created for each of the eight participants using data normalized to Montreal Neurological Institute (MNI) space. The resting state networks (RSN) were then found by performing a one sample T-test on group level. Six seed-coordinates, based on literature, where used revealing the the homotopic connections in anterior Hippocampus, Motor cortex, Dorsal attention, Visual and the Default mode network (DMN) as well for an anterior-posterior connection in the DMN.

    By comparing the maximum T-values within the regions for the RSN no systematic difference could be found between the multiband and conventional fMRI data. Further tests were conducted to evaluate if the sequences would differentiate in their results if the acquisition time was shortened, i.e shortening the time-series in the voxels. However no such difference could be established.Importantly, the results are specific to the 32 channel head coil used in the current study. Presumably recently available and improved coil designs could better exploit the multiband technique.

  • 26.
    Blusi, Madeleine
    et al.
    Umeå University, Faculty of Medicine, Department of Community Medicine and Rehabilitation. Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Nieves, Juan Carlos
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Feasibility and Acceptability of Smart Augmented Reality Assisting Patients with Medication Pillbox Self-Management2019In: Studies in Health Technology and Informatics, ISSN 0926-9630, E-ISSN 1879-8365, p. 521-525Article in journal (Refereed)
    Abstract [en]

    Complex prescribed medicine regimens require extensive self-management. Handling multiple pills can be confusing; using a pillbox organiser is a common strategy. A smart Medication Coach Intelligent Agent (MCIA) can support patients in handling medicine. The aim of this research was to evaluate the feasibility and acceptability of the MCIA. A prototype was tested with 15 participants, age 17-76, filled a pillbox according to prescription assisted by the MCIA implemented in a Microsoft HoloLens. A quantitative method using questionnaires was applied. Results showed that using the MCIA implemented in an AR-headset, to assist people with prescribed polypharmacy regimen in filling a pillbox, was feasible and acceptable. There was a difference related to age regarding people's willingness to use an AR-headset for medication self-management. People older than 65 felt less comfortable using the technology and were also more hesitant to use the technology than those under 65.

  • 27.
    Bodén, Ida
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Surgery.
    Nilsson, David
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Naredi, Peter
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Surgery.
    Lindholm-Sethson, Britta
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF).
    Characterization of healthy skin using near infrared spectroscopy and skin impedance2008In: Medical and Biological Engineering and Computing, ISSN 0140-0118, E-ISSN 1741-0444, Vol. 46, no 10, p. 985-995Article in journal (Refereed)
    Abstract [en]

    Near infrared spectroscopy (NIR) and skin impedance (IMP) spectroscopy are two methods suggested for diagnoses of diseases inducing adverse effects in skin. The reproducibility of these methods and their potential value in non-invasive diagnostics were investigated. Measurements were performed in vivo on healthy skin at five anatomic body sites on eight young women. partial least squares discriminant analysis showed that both methods were useful for classification of the skin characteristics at the sites. Inter-individually the NIR model gave 100% correct classification while the IMP model provided 92%. Intra-individually the NIR model gave 88% correct classification whereas the IMP model did not provide any useful classification. The correct classification was increased to 93% when both datasets were combined, which demonstrates the value of adding information. Partial least squares discriminant analysis gave 72% correct predictions of skin sites while the combined model slightly improved to 73%.

  • 28.
    Bodén, Ida
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Surgery.
    Nyström, Josefina
    Swedish University of Agricultural Sciences, Unit of Biomass Technology and Chemistry.
    Lundskog, Bertil
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Zazo, Virginia
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Dermatology and Venerology.
    Geladi, Paul
    Swedish University of Agricultural Sciences, Unit of Biomass Technology and Chemistry.
    Lindholm-Sethson, Britta
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Naredi, Peter
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Surgery.
    Non-invasive identification of melanoma with near-infrared and skin impedance spectroscopy2013In: Skin research and technology, ISSN 0909-752X, E-ISSN 1600-0846, Vol. 19, no 1, p. e473-e478Article in journal (Refereed)
    Abstract [en]

    Background/purpose: An early diagnosis of cutaneous malignant melanoma is of high importance for good prognosis. An objective, non-invasive instrument could improve the diagnostic accuracy of melanoma and decrease unnecessary biopsies. The aim of this study was to investigate the use of Near infrared and skin impedance spectroscopy in combination as a tool to distinguish between malignant and benign skin tumours.

    Methods: Near infrared and skin impedance spectra were collected in vivo on 50 naevi or suspect melanomas prior to excision. Received data was analysed with multivariate techniques and the results were compared to histopathology analyses of the tumours. A total of 12 cutaneous malignant melanomas, 19 dysplastic naevi and 19 benign naevi were included in the study.

    Results: The observed sensitivity and specificity of the proposed method were 83% and 95%, respectively, for malignant melanoma.

    Conclusions: The results indicate that the combination of near infrared and skin impedance spectroscopy is a promising tool for non-invasive diagnosis of suspect cutaneous malignant melanomas. 

  • 29.
    Brantefors, Per
    Umeå University, Faculty of Medicine, Department of Radiation Sciences. Umeå University, Faculty of Science and Technology, Department of Physics. Karolinska Institutet, Department of Clinical Neuroscience.
    Dynamic fMRI brain connectivity: A study of the brain’s large-scale network dynamics2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Approximately 20% of the body’s energy consumption is ongoingly consumed by the brain, where the main part is due to the neural activity, which is only increased slightly when doing a demanding task. This ongoingly neural activity are studied with the so called resting-state fMRI, which mean that the neural activity in the brain is measured for participants with no specific task. These studies have been useful to understand the neural function and how the neural networks are constructed and cooperate. This have also been helpful in several clinical research, for example have differences been identified between bipolar disorder and major depressive disorder. Recent research has focused on temporal properties of the ongoing activity and it is well known that neural activity occurs in bursts. In this study, resting-state fMRI data and temporal graph theory is used to develop a point based method (PBM) to quantify these bursts at a nodal level. By doing this, the bursty pattern can be further investigated and the nodes showing the most bursty pattern (i.e hubs) can be identified. The method developed shows a robustness regarding several different aspects. In the method is two different variance threshold algorithms suggested. One local variance threshold (LVT) based on the individual variance of the edge time-series and one global variance threshold (GVT) based on the variance of all edges time-series, where the GVT shows the highest robustness. However, the choice of threshold needs to be adapted for the aims of the current study. Finally, this method ends up in a new measure to quantify this bursty pattern named bursty centrality. The derived temporal graph theoretical measure was correlated with traditional static graph properties used in resting state and showed a low but significant correlation. By applying this method on resting-state fMRI data for 32 young adults was it possible to identify regions of the brain that showed the most dynamic properties, these regions differed between the two thresholding algorithms

  • 30. Brolin, Gustav
    et al.
    Edenbrandt, Lars
    Granerus, Goeran
    Olsson, Anna
    Afzelius, David
    Gustafsson, Agneta
    Jonsson, Cathrine
    Hagerman, Jessica
    Johansson, Lena
    Riklund, Katrine
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology. EQUALIS AB, Uppsala, Sweden.
    Ljungberg, Michael
    The accuracy of quantitative parameters in Tc-99m-MAG3 dynamic renography: a national audit based on virtual image data2016In: Clinical Physiology and Functional Imaging, ISSN 1475-0961, E-ISSN 1475-097X, Vol. 36, no 2, p. 146-154Article in journal (Refereed)
    Abstract [en]

    Assessment of image analysis methods and computer software used in Tc-99m-MAG3 dynamic renography is important to ensure reliable study results and ultimately the best possible care for patients. In this work, we present a national multicentre study of the quantification accuracy in Tc-99m-MAG3 renography, utilizing virtual dynamic scintigraphic data obtained by Monte Carlo-simulated scintillation camera imaging of digital phantoms with time-varying activity distributions. Three digital phantom studies were distributed to the participating departments, and quantitative evaluation was performed with standard clinical software according to local routines. The differential renal function (DRF) and time to maximum renal activity (T-max) were reported by 21 of the 28 Swedish departments performing Tc-99m-MAG3 studies as of 2012. The reported DRF estimates showed a significantly lower precision for the phantom with impaired renal uptake than for the phantom with normal uptake. The T-max estimates showed a similar trend, but the difference was only significant for the right kidney. There was a significant bias in the measured DRF for all phantoms caused by different positions of the left and right kidney in the anterior-posterior direction. In conclusion, this study shows that virtual scintigraphic studies are applicable for quality assurance and that there is a considerable uncertainty associated with standard quantitative parameters in dynamic Tc-99m-MAG3 renography, especially for patients with impaired renal function.

  • 31.
    Brynolfsson, Patrik
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Using radial k-space sampling and temporal filters in MRI to improve temporal resolution2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

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

  • 32.
    Brynolfsson, Patrik
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Yu, Jun
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Wirestam, Ronnie
    Lund University.
    Karlsson, Mikael
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Garpebring, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences. CJ Gorter Center for High Field MRI, Leiden University Medical Center, Leiden, Netherlands.
    Combining phase and magnitude information for contrast agent quantification in dynamic contrast-enhanced MRI using statistical modeling2015In: Magnetic Resonance in Medicine, ISSN 0740-3194, E-ISSN 1522-2594, Vol. 74, no 4, p. 1156-1164Article in journal (Refereed)
    Abstract [en]

    Purpose: The purpose of this study was to investigate, using simulations, a method for improved contrast agent (CA) quantification in DCE-MRI.

    Methods: We developed a maximum likelihood estimator that combines the phase signal in the DCE-MRI image series with an additional CA estimate, e.g. the estimate obtained from magnitude data. A number of simulations were performed to investigate the ability of the estimator to reduce bias and noise in CA estimates. Noise levels ranging from that of a body coil to that of a dedicated head coil were investigated at both 1.5T and 3T.

    Results: Using the proposed method, the root mean squared error in the bolus peak was reduced from 2.24 to 0.11 mM in the vessels and 0.16 to 0.08 mM in the tumor rim for a noise level equivalent of a 12-channel head coil at 3T. No improvements were seen for tissues with small CA uptake, such as white matter.

    Conclusion: Phase information reduces errors in the estimated CA concentrations. A larger phase response from higher field strengths or higher CA concentrations yielded better results. Issues such as background phase drift need to be addressed before this method can be applied in vivo.

  • 33. Bujila, Robert
    et al.
    Kull, Love
    Danielsson, Mats
    Andersson, Jonas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Applying three different methods of measuring CTDIfree air to the extended CTDI formalism for wide-beam scanners (IEC 60601-2-44): a comparative study2018In: Journal of Applied Clinical Medical Physics, ISSN 1526-9914, E-ISSN 1526-9914, Vol. 19, no 4, p. 281-289Article in journal (Refereed)
    Abstract [en]

    Purpose: The weighted CT dose index (CTDIw) has been extended for a nominal total collimation width (nT) greater than 40 mm and relies on measurements of CTDfree air. The purpose of this work was to compare three methods of measuring CTDIfree air and subsequent calculations of CTDIw to investigate their clinical appropriateness.

    Methods: The CTDIfree air, for multiple nTs up to 160 mm, was calculated from (1) high-resolution air kerma profiles from a step-and-shoot translation of a liquid ionization chamber (LIC) (considered to be a dosimetric reference), (2) pencil ionization chamber (PIC) measurements at multiple contiguous positions, and (3) air kerma profiles obtained through the continuous translation of a solid-state detector. The resulting CTDIfree air was used to calculate the CTDIw, per the extended formalism, and compared.

    Results: The LIC indicated that a 40 mm nT should not be excluded from the extension of the CTDIw formalism. The solid-state detector differed by as much as 8% compared to the LIC. The PIC was the most straightforward method and gave equivalent results to the LIC.

    Conclusions: The CTDIw calculated with the latest CTDI formalism will differ most for 160 mm nTs (e.g., whole-organ perfusion or coronary CT angiography) compared to the previous CTDI formalism. Inaccuracies in the measurement of CTDIfree air will subsequently manifest themselves as erroneous calculations of the CTDIw, for nTs greater than 40 mm, with the latest CTDI formalism. The PIC was found to be the most clinically feasible method and was validated against the LIC.

  • 34.
    Bäcklund, Tomas
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Development and validation of a system for clinical assessment of gait cycle parameter in patients with idiopathic normal pressure hydocephalus2013Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A number of parameters have been identified as characteristic of the walking pattern in patients with INPH. Most of these have been identified through qualitative surveys and manually conducted test batteries. In order to obtain quantitative, standardized and objective measures, which enable studies based on larger patient populations and comparable results, there is a need for a user-friendly system that can measure specific key parameters over time in a reliable manner in everyday clinical work. Step height, width and the variability in the gait cycle are such parameters which are interesting research areas for this group of patient.

    Problems with balance and gait are very common in other patient groups as well, particularly in neurological diseases such as Parkinson's disease, multiple sclerosis and stroke.

    This is the reason that the development of this gait analyzer is performed. Giving access to a simple and objective method for estimating gait and balance ability in clinical routine investigations would increase the ability to provide the right kind of treatment, confirm treatment results, and conducting larger research studies. Therefore, this equipment can contribute to the assessment of diseases which contain impaired gait. As a first test of the usability and for the validation of accuracy and repeatability of the equipment a group of healthy volunteers was used. Results from tests on healthy subjects show god repeatability between measurements, for step width at normal gait the difference was -0,2 ±0,34 cm (mean, ±SD) and step height 0,69 ±3,34 cm. The stride time variability in the healthy group where very small 0,00048 ±0,00028 s2 with a difference between test of 0,000019 ±0,00038 s2. Three pilot patients have been tested where we have clearly seen indications of increased stride time variability and reduced step height.

  • 35.
    Bölenius, Karin
    et al.
    Umeå University, Faculty of Medicine, Department of Nursing.
    Brulin, Christine
    Umeå University, Faculty of Medicine, Department of Nursing.
    Grankvist, Kjell
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Clinical chemistry.
    Lindkvist, Marie
    Umeå University, Faculty of Medicine, Department of Public Health and Clinical Medicine, Epidemiology and Global Health.
    Söderberg, Johan
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Clinical chemistry.
    A content validated questionnaire for assessment of self reported venous blood sampling practices2012In: BMC Research Notes, ISSN 1756-0500, E-ISSN 1756-0500, Vol. 5, p. 39-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Venous blood sampling is a common procedure in health care. It is strictly regulated by national and international guidelines. Deviations from guidelines due to human mistakes can cause patient harm. Validated questionnaires for health care personnel can be used to assess preventable "near misses"--i.e. potential errors and nonconformities during venous blood sampling practices that could transform into adverse events. However, no validated questionnaire that assesses nonconformities in venous blood sampling has previously been presented. The aim was to test a recently developed questionnaire in self reported venous blood sampling practices for validity and reliability.

    FINDINGS: We developed a questionnaire to assess deviations from best practices during venous blood sampling. The questionnaire contained questions about patient identification, test request management, test tube labeling, test tube handling, information search procedures and frequencies of error reporting. For content validity, the questionnaire was confirmed by experts on questionnaires and venous blood sampling. For reliability, test-retest statistics were used on the questionnaire answered twice. The final venous blood sampling questionnaire included 19 questions out of which 9 had in total 34 underlying items. It was found to have content validity. The test-retest analysis demonstrated that the items were generally stable. In total, 82% of the items fulfilled the reliability acceptance criteria.

    CONCLUSIONS: The questionnaire could be used for assessment of "near miss" practices that could jeopardize patient safety and gives several benefits instead of assessing rare adverse events only. The higher frequencies of "near miss" practices allows for quantitative analysis of the effect of corrective interventions and to benchmark preanalytical quality not only at the laboratory/hospital level but also at the health care unit/hospital ward.

  • 36.
    Börlin, Niclas
    et al.
    Umeå University, Faculty of Science and Technology, Department of Computing Science.
    Thien, Truike
    Katholieke Universiteit Nijmegen, Nijmegen, Holland.
    Kärrholm, Johan
    Sahlgrenska University Hospital, Göteborg, Sweden.
    The precision of radiostereometric measurements: manual vs. digital measurements2002In: Journal of Biomechanics, ISSN 0021-9290, E-ISSN 1873-2380, Vol. 35, no 1, p. 69-79Article in journal (Refereed)
    Abstract [en]

    The precision of digital vs. manual radiostereometric measurements in total hip arthroplasty was evaluated using repeated stereoradiographic exposures with an interval of 10–15 min. Ten Lubinus SP2 stems cemented into bone specimens and 12 patients with the same stem design were used to evaluate the precision of stem translations and rotations. The precision of translations and rotations of the cup and femoral head penetration was studied in 12 patients with whole polyethylene cups.

    The use of a measurement method based on digitised radiographs improved the precision for some of the motion parameters, whereas many of them did not change. A corresponding pattern was observed for both the intra- and interobserver error. Of the wear parameters, the most pronounced improvements were the 3D wear and in the proximal-distal direction, although the anterior-posterior precision was also improved. The mean errors of rigid body and elliptic fitting decreased in all evaluations but one, consistent with a more reproducible identification of the markers centres and the edge of the femoral head.

    Increased precision of radiostereometric measurements may be used to increase the statistical power of future randomised studies and to study new fields in orthopaedics requiring higher precision than has been available with RSA based on manual measurements.

  • 37.
    Candefjord, Stefan
    et al.
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Nyberg, Morgan
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Jalkanen, Ville
    Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF). Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Ramser, Kerstin
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Lindahl, Olof
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Combining fibre optic Raman spectroscopy and tactile resonance measurement for tissue characterization2010In: Measurement science and technology, ISSN 0957-0233, E-ISSN 1361-6501, Vol. 21, no 125801, p. 1-8Article in journal (Refereed)
    Abstract [en]

    Tissue characterization is fundamental for identification of pathological conditions. Raman spectroscopy (RS) and tactile resonance measurement (TRM) are two promising techniques that measure biochemical content and stiffness, respectively. They have potential to complement the golden standard-–histological analysis. By combining RS and TRM, complementary information about tissue content can be obtained and specific drawbacks can be avoided. The aim of this study was to develop a multivariate approach to compare RS and TRM information. The approach was evaluated on measurements at the same points on porcine abdominal tissue. The measurement points were divided into five groups by multivariate analysis of the RS data. A regression analysis was performed and receiver operating characteristic (ROC) curves were used to compare the RS and TRM data. TRM identified one group efficiently (area under ROC curve 0.99). The RS data showed that the proportion of saturated fat was high in this group. The regression analysis showed that stiffness was mainly determined by the amount of fat and its composition. We concluded that RS provided additional, important information for tissue identification that was not provided by TRM alone. The results are promising for development of a method combining RS and TRM for intraoperative tissue characterization.

  • 38.
    Candefjord, Stefan
    et al.
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Nyberg, Morgan
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Jalkanen, Ville
    Umeå University, Faculty of Science and Technology, Applied Physics and Electronics. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics.
    Ramser, Kerstin
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Lindahl, Olof
    Dept. of Computer Science and Electrical Engineering, Luleå University of Technology.
    Evaluating the use of a Raman fiberoptic probe in conjunction with a resonance sensor for measuring porcine tissue in vitro2009In: IFMBE Proceedings of the World Congress on Medical Physics and Biomedical Engineering, Heidelberg: Springer , 2009, p. 414-417Conference paper (Refereed)
    Abstract [en]

    Prostate cancer is the most common form of cancer and is the third leading cause of cancer-related death in European men. There is a need for new methods that can accurately localize and diagnose prostate cancer. In this study a new approach is presented: a combination of resonance sensor technology and Raman spectroscopy. Both methods have shown promising results for prostate cancer detection in vitro. The aim of this study was to evaluate the combined information from measurements with a Raman fiberoptic probe and a resonance sensor system. Pork belly tissue was used as a model system. A three-dimensional translation table was equipped with an in-house developed software, allowing measurements to be performed at the same point using two separate instruments. The Raman data was analyzed using principal component analysis and hierarchical clustering analysis. The spectra were divided into 5 distinct groups. The mean stiffness of each group was calculated from the resonance sensor measurements. One of the groups differed significantly (p < 0.05) from the others. A regression analysis, with the stiffness parameter as response variable and the principal component scores of the Raman data as the predictor variables, explained 67% of the total variability. The use of a smaller resonance sensor tip would probably increase the degree of correlation. In conclusion, Raman spectroscopy provides additional discriminatory power to the resonance sensor.

  • 39. Chen, Hanwei
    et al.
    Jiang, Jinzhao
    Gao, Junling
    Liu, Dan
    Axelsson, Jan
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Cui, Minyi
    Gong, Nan-Jie
    Feng, Shi-Ting
    Luo, Liangping
    Huang, Bingsheng
    Tumor Volumes Measured From Static and Dynamic F-18-fluoro-2-deoxy-D-glucose Positron Emission Tomography-Computed Tomography Scan: Comparison of Different Methods Using Magnetic Resonance Imaging as the Criterion Standard2014In: Journal of computer assisted tomography, ISSN 0363-8715, E-ISSN 1532-3145, Vol. 38, no 2, p. 209-215Article in journal (Refereed)
    Abstract [en]

    Objective: The objective of this study was to compare the accuracy of calculating the primary tumor volumes using a gradient-based method and fixed threshold methods on the standardized uptake value (SUV) maps and the net influx of FDG (Ki) maps from positron emission tomography-computed tomography (PET-CT) images. Materials and Methods: Newly diagnosed patients with head and neck cancer were recruited, and dynamic PET-CT scan and T2-weighted magnetic resonance imaging were performed. The maps of Ki and SUV were calculated from PET-CT images. The tumor volumes were calculated using a gradient-based method and a fixed threshold method at 40% of maximal SUV or maximal Ki. Four kinds of volumes, VOLKi-Gra (from the Ki maps using the gradient-based method), VOLKi-40% (from the Ki maps using the threshold of 40% maximal Ki), VOLSUV-Gra (from the SUV maps using the gradient-based method), and VOLSUV-40% (from the SUV maps using the threshold of 40% maximal SUV), were acquired and compared with VOLMRI (the volumes acquired on T2-weighted images) using the Pearson correlation, paired t test, and similarity analysis. Results: Eighteen patients were studied, of which 4 had poorly defined tumors (PDT). The positron emission tomography-derived volumes were as follows: VOLSUV-40%, 2.1 to 41.2 cm(3) (mean [SD], 12.3 [10.6]); VOLSUV-Gra, 2.2 to 28.1 cm(3) (mean [SD], 13.2 [8.4]); VOLKi-Gra, 2.4 to 17.0 cm(3) (mean [SD], 9.5 [4.6]); and VOLKi-40%, 2.7 to 20.3 cm(3) (mean [SD], 12.0 [6.0]). The VOLMRI ranged from 2.9 to 18.1 cm(3) (mean [SD], 9.1 [3.9]). The VOLKi-Gra significantly correlated with VOLMRI with the highest correlation coefficient (PDT included, R = 0.673, P = 0.002; PDT excluded, R = 0.841, P < 0.001) and presented no difference from VOLMRI (P = 0.672 or 0.561, respectively, PDT included and excluded). The difference between VOLKi-Gra and VOLMRI was also the smallest. Conclusions: The tumor volumes delineated on the Ki maps using the gradient-based method are more accurate than those on the SUV maps and using the fixed threshold methods.

  • 40. Clemente, Francesco
    et al.
    D'Alonzo, Marco
    Controzzi, Marco
    Edin, Benoni B.
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB), Physiology.
    Cipriani, Christian
    Non-Invasive, Temporally Discrete Feedback of Object Contact and Release Improves Grasp Control of Closed-Loop Myoelectric Transradial Prostheses2016In: IEEE transactions on neural systems and rehabilitation engineering, ISSN 1534-4320, E-ISSN 1558-0210, Vol. 24, no 12, p. 1314-1322Article in journal (Refereed)
    Abstract [en]

    Human grasping and manipulation control critically depends on tactile feedback. Without this feedback, the ability for fine control of a prosthesis is limited in upper limb amputees. Although various approaches have been investigated in the past, at present there is no commercially available device able to restore tactile feedback in upper limb amputees. Based on the Discrete Event-driven Sensory feedback Control (DESC) policy we present a device able to deliver short-lasting vibrotactile feedback to transradial amputees using commercially available myoelectric hands. The device (DESC-glove) comprises sensorized thimbles to be placed on the prosthesis digits, a battery-powered electronic board, and vibrating units embedded in an arm-cuff being transiently activated when the prosthesis makes and breaks contact with objects. The consequences of using the DESC-glove were evaluated in a longitudinal study. Five transradial amputees were equipped with the device for onemonth at home. Through a simple test proposed here for the first time-the virtual eggs test-we demonstrate the effectiveness of the device for prosthetic control in daily life conditions. In the future the device could be easily exploited as an add-on to complement myoelectric prostheses or even embedded in prosthetic sockets to enhance their control by upper limb amputees.

  • 41. Cronskär, Marie
    et al.
    Rännar, Lars-Erik
    Bäckström, Mikael
    Nilsson, Kjell G
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Orthopaedics.
    Samuelsson, Börje
    Patient-Specific Clavicle Reconstruction Using Digital Design and Additive Manufacturing2015In: Journal of mechanical design (1990), ISSN 1050-0472, E-ISSN 1528-9001, Vol. 137, no 11, article id 111418Article in journal (Refereed)
    Abstract [en]

    There is a trend toward operative treatment for certain types of clavicle fractures and these are usually treated with plate osteosynthesis. The subcutaneous location of the clavicle makes the plate fit important, but the clavicle has a complex shape, which varies greatly between individuals and hence standard plates often have a poor fit. Using computed tomography (CT) based design, the plate contour and screw positioning can be optimized to the actual case. A method for patient-specific plating using design based on CT-data, additive manufacturing (AM), and postprocessing was initially evaluated through three case studies, and the plate fit on the reduced fracture was tested during surgery (then replaced by commercial plates). In all three cases, the plates had an adequate fit on the reduced fracture. The time span from CT scan of the fracture to final implant was two days. An approach to achieve functional design and screw-hole positioning was initiated. These initial trials of patient-specific clavicle plating using AM indicate the potential for a smoother plate with optimized screw positioning. Further, the approach facilitates the surgeon's work and operating time can be saved.

  • 42. Desmarais, Samantha M.
    et al.
    Cava, Felipe
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    de Pedro, Miguel A.
    Huang, Kerwyn Casey
    Isolation and preparation of bacterial cell walls for compositional analysis by Ultra Performance Liquid Chromatography2014In: Journal of Visualized Experiments, ISSN 1940-087X, E-ISSN 1940-087X, no 83, p. UNSP e51183-Article in journal (Refereed)
    Abstract [en]

    The bacterial cell wall is critical for the determination of cell shape during growth and division, and maintains the mechanical integrity of cells in the face of turgor pressures several atmospheres in magnitude. Across the diverse shapes and sizes of the bacterial kingdom, the cell wall is composed of peptidoglycan, a macromolecular network of sugar strands crosslinked by short peptides. Peptidoglycan's central importance to bacterial physiology underlies its use as an antibiotic target and has motivated genetic, structural, and cell biological studies of how it is robustly assembled during growth and division. Nonetheless, extensive investigations are still required to fully characterize the key enzymatic activities in peptidoglycan synthesis and the chemical composition of bacterial cell walls. High Performance Liquid Chromatography (HPLC) is a powerful analytical method for quantifying differences in the chemical composition of the walls of bacteria grown under a variety of environmental and genetic conditions, but its throughput is often limited. Here, we present a straightforward procedure for the isolation and preparation of bacterial cell walls for biological analyses of peptidoglycan via HPLC and Ultra Performance Liquid Chromatography (UPLC), an extension of HPLC that utilizes pumps to deliver ultra-high pressures of up to 15,000 psi, compared with 6,000 psi for HPLC. In combination with the preparation of bacterial cell walls presented here, the low-volume sample injectors, detectors with high sampling rates, smaller sample volumes, and shorter run times of UPLC will enable high resolution and throughput for novel discoveries of peptidoglycan composition and fundamental bacterial cell biology in most biological laboratories with access to an ultracentrifuge and UPLC.

  • 43.
    Dunås, Tora
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Blood flow assessment in cerebral arteries with 4D flow magnetic resonance imaging: an automatic atlas-based approach2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Background: Disturbed blood flow to the brain has been associated with several neurological diseases, from stroke and vascular diseases to Alzheimer’s and cognitive decline. To determine the cerebral arterial blood flow distribution, measurements are needed in both distal and proximal arteries.

    4D flow MRI makes it possible to obtain blood flow velocities from a volume covering the entire brain in one single scan. This facilitates more extensive flow investigations, since flow rate assessment in specific arteries can be done during post-processing. The flow rate assessment is still rather laborious and time consuming, especially if the number of arteries of interest is high. In addition, the quality of the measurements relies heavily on the expertise of the investigator.

    The aim of this thesis was to develop and evaluate an automatic post-processing tool for 4D flow MRI that identifies the main cerebral arteries and calculates their blood flow rate with minimal manual input. Atlas-based labeling of brain tissue is common in toolboxes for analysis of neuroimaging-data, and we hypothesized that a similar approach would be suitable for arterial labeling. We also wanted to investigate how to best separate the arterial lumen from background for calculation of blood flow.

    Methods: An automatic atlas-based arterial identification method (AAIM) for flow assessment was developed. With atlas-based labeling, voxels are labeled based on their spatial location in MNI-space, a stereotactic coordinate system commonly used for neuroimaging analysis. To evaluate the feasibility of this approach, a probabilistic atlas was created from a set of angiographic images derived from 4D flow MRI. Included arteries were the anterior (ACA), middle (MCA) and posterior (PCA) cerebral arteries, as well as the internal carotid (ICA), vertebral (VA), basilar (BA) and posterior communicating (PCoA) arteries. To identify the arteries in an angiographic image, a vascular skeleton where each branch represented an arterial segment was extracted and labeled according to the atlas. Labeling accuracy of the AAIM was evaluated by visual inspection.

    Next, the labeling method was adapted for flow measurements by pre-defining desired regions within the atlas. Automatic flow measurements were then compared to measurements at manually identified locations. During the development process, arterial identification was evaluated on four patient cohorts, with and without vascular disease. Finally, three methods for flow quantification using 4D flow MRI: k-means clustering; global thresholding; and local thresholding, were evaluated against a standard reference method.

    Results: The labeling accuracy on group level was between 96% and 87% for all studies, and close to 100% for ICA and BA. Short arteries (PCoA) and arteries with large individual anatomical variation (VA) were the most challenging. Blood flow measurements at automatically identified locations were highly correlated (r=0.99) with manually positioned measurements, and difference in mean flow was negligible.

    Both global and local thresholding out-performed k-means clustering, since the threshold value could be optimized to produce a mean difference of zero compared to reference. The local thresholding had the best concordance with the reference method (p=0.009, F-test) and was the only method that did not have a significant correlation between flow difference and flow rate. In summary, with a local threshold of 20%, ICC was 0.97 and the flow rate difference was -0.04 ± 15.1 ml/min, n=308.

    Conclusion: This thesis work demonstrated that atlas-based labeling was suitable for identification of cerebral arteries, enabling automated processing and flow assessment in 4D flow MRI. Furthermore, the proposed flow rate quantification algorithm reduced some of the most important shortcomings associated with previous methods. This new platform for automatic 4D flow MRI data analysis fills a gap needed for efficient in vivo investigations of arterial blood flow distribution to the entire vascular tree of the brain, and should have important applications to practical use in neurological diseases.

  • 44.
    Dunås, Tora
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Holmgren, Madelene
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Wåhlin, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences. Umeå University, Faculty of Medicine, Umeå Centre for Functional Brain Imaging (UFBI).
    Malm, Jan
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Neuroscience.
    Eklund, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences. Umeå University, Faculty of Medicine, Umeå Centre for Functional Brain Imaging (UFBI).
    Accuracy of blood flow assessment in cerebral arteries with 4D flow MRI: Evaluation with three segmentation methods2019In: Journal of Magnetic Resonance Imaging, ISSN 1053-1807, E-ISSN 1522-2586, Vol. 50, no 2, p. 511-518Article in journal (Refereed)
    Abstract [en]

    Background: Accelerated 4D flow MRI allows for high‐resolution velocity measurements with whole‐brain coverage. Such scans are increasingly used to calculate flow rates of individual arteries in the vascular tree, but detailed information about the accuracy and precision in relation to different postprocessing options is lacking.

    Purpose: To evaluate and optimize three proposed segmentation methods and determine the accuracy of in vivo 4D flow MRI blood flow rate assessments in major cerebral arteries, with high‐resolution 2D PCMRI as a reference.

    Study Type: Prospective.

    Subjects: Thirty‐five subjects (20 women, 79 ± 5 years, range 70–91 years).

    Field Strength/Sequence: 4D flow MRI with PC‐VIPR and 2D PCMRI acquired with a 3 T scanner.

    Assessment: We compared blood flow rates measured with 4D flow MRI, to the reference, in nine main cerebral arteries. Lumen segmentation in the 4D flow MRI was performed with k‐means clustering using four different input datasets, and with two types of thresholding methods. The threshold was defined as a percentage of the maximum intensity value in the complex difference image. Local and global thresholding approaches were used, with evaluated thresholds from 6–26%.

    Statistical Tests: Paired t‐test, F‐test, linear correlation (P < 0.05 was considered significant) along with intraclass correlation (ICC).

    Results: With the thresholding methods, the lowest average flow difference was obtained for 20% local (0.02 ± 15.0 ml/min, ICC = 0.97, n = 310) or 10% global (0.08 ± 17.3 ml/min, ICC = 0.97, n = 310) thresholding with a significant lower standard deviation for local (F‐test, P = 0.01). For all clustering methods, we found a large systematic underestimation of flow compared with 2D PCMRI (16.1–22.3 ml/min).

    Data Conclusion: A locally adapted threshold value gives a more stable result compared with a globally fixed threshold. 4D flow with the proposed segmentation method has the potential to become a useful reliable clinical tool for assessment of blood flow in the major cerebral arteries.

    Level of Evidence: 2

    Technical Efficacy: Stage 2

  • 45.
    Dunås, Tora
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences. Umeå Universitet.
    Wåhlin, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences. Umeå University, Faculty of Medicine, Umeå Centre for Functional Brain Imaging (UFBI).
    Zarrinkoob, Laleh
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Neuroscience.
    Malm, Jan
    Umeå University, Faculty of Medicine, Department of Pharmacology and Clinical Neuroscience, Clinical Neuroscience.
    Eklund, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences. Umeå University, Faculty of Medicine, Umeå Centre for Functional Brain Imaging (UFBI).
    4D flow MRI: automatic assessment of blood flow in cerebral arteries2019In: Biomedical Physics & Engineering Express, ISSN 2057-1976, Vol. 5, no 1, article id 015003Article in journal (Refereed)
    Abstract [en]

    Objective: With a 10-minute 4D flow MRI scan, the distribution of blood flow to individual arteries throughout the brain can be analyzed. This technique has potential to become a biomarker for treatment decisions, and to predict prognosis after stroke. To efficiently analyze and model the large dataset in clinical practice, automatization is needed. We hypothesized that identification of selected arterial regions using an atlas with a priori probability information on their spatial distribution can provide standardized measurements of blood flow in the main cerebral arteries.

    Approach: A new method for automatic placement of measurement locations in 4D flow MRI was developed based on an existing atlas-based method for arterial labeling, by defining specific regions of interest within the corresponding arterial atlas. The suggested method was evaluated on 38 subjects with carotid artery stenosis, by comparing measurements of blood flow rate at automatically selected locations to reference measurements at manually selected locations.

    Main results: Automatic and reference measurement ranged from 10 to 580 ml min−1 and were highly correlated (r = 0.99) with a mean flow difference of 0.61 ± 10.7 ml min−1 (p = 0.21). Out of the 559 arterial segments in the manual reference, 489 were correctly labeled, yielding a sensitivity of 88%, a specificity of 85%, and a labeling accuracy of 87%.

    Significance: This study confirms that atlas-based labeling of 4D flow MRI data is suitable for efficient flow quantification in the major cerebral arteries. The suggested method improves the feasibility of analyzing cerebral 4D flow data, and fills a gap necessary for implementation in clinical use.

  • 46.
    Duvaldt, Maria
    Umeå University, Faculty of Science and Technology, Department of Physics. Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics. Umeå University, Faculty of Science and Technology, Centre for Biomedical Engineering and Physics (CMTF). Karolinska Universitetssjukhuset Huddinge.
    Developing a Semi-Automatised Tool for Grading Brain Tumours with Susceptibility-Weighted MRI2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Gliomas are a common type of brain tumour and for the treatment of a patient it is important to determine the tumour’s grade of malignancy. This is done today by a biopsy, a histopathological analysis of the tumourous tissue, that is classified by the World Health Organization on a malignancy scale from I to IV. Recent studies have shown that the local image variance (LIV) and the intratumoural susceptibility signal (ITSS) in susceptibility-weighted MR images correlate to the tumour grade. This thesis project aims to develop a software program as aid for the radiologists when grading a glioma. The software should by image analysis be able to separate the gliomas into low grade (I-II) and high grade (III-IV). The result is a graphical user interface written in Python 3.4.3. The user chooses an image, draws a region of interest and starts the analysis. The analyses implemented in the program are LIV and ITSS mentioned above, and the code can be extended to contain other types of analyses as research progresses. To validate the image analysis, 16 patients with glioma grades confirmed by biopsy are included in the study. Their susceptibility-weighted MR images were analysed with respect to LIV and ITSS, and the outcome of those image analyses was tested versus the known grades of the patients. No statistically significant difference could be seen between the high and the low grade group, in the case of LIV. This was probably due to hemorrhage and calcification, characteristic for some tumours and interpreted as blood vessels. Concerning ITSS a statistically significant difference could be seen between the high and the low grade group (p < 0.02). The sensitivity and specificity was 80% and 100% respec- tively. Among these 16 gliomas, 11 were astrocytic tumours and between low and high grade astrocytomas a statistically significant difference was shown. The degree of LIV was significantly different between the two groups (p < 0.03) and the sensitivity and specificity were 86% and 100% respectively. The degree of ITSS was significantly different between the two groups (p < 0.04) and the sensitivity and specificity were 86% and 100% respectively. Spearman correlation showed a correlation between LIV and tumour grade (for all gliomas r = 0.53 and p < 0.04, for astrocytomas r = 0.84 and p < 0.01). A correlation was also found between ITSS and tumour grade (for all gliomas r = 0.69 and p < 0.01, for astrocytomas r = 0.63 and p < 0.04). The results indicate that SWI is useful for distinguishing between high and low grade astrocytoma with 1.5T imaging within this cohort. It also seems possible to distinguish between high and low grade glioma with ITSS.

  • 47.
    Edling, Pontus
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics. Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Enkel UV-absorptionsfotometer för absorbansmätning i medicinska prover2019Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In laboratory medicine there is equipment such as the spectralphotometer that can measure absorption in a solution to determine the concentration of proteins, amino acids and the like. This is an often expensive equipment and often not readily available. The Department of Biomedical Engineering - Research and Development (BE-RD) at University hospital of Umeå has been asked to investigate the possibilities of constructing a simple and cheap UV-absorption photometer. The aim of this study was to produce a functioning prototype of a UV-absorption photometer that would be able to measure the concentration of SAICA-r and S-Ado which occurs in the urine of the rare disease Adenolosuccinate lyase deficiency (ASL). For this bachelor thesis, adenosine triphosphate (ATP) was chosen as measuring substance, since ATP is a stable protein which is soluble in water and which can be frozen and defrosted. It also has an absorbance spectra which is very close to SAICA-r and S-Ado. A functioning prototype of the UV-absorption photometer has been developed. The prototype demonstrates a good linearity(R2 = 0.9956) for concentrations between 0-50 mg/L and a high accuracy for absorbance σ=0.0006. With these results, the prototype is judged to be capable of measuring the content of SAICAr and S-Ado in a urine sample.

  • 48.
    Edman, Agnes
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Optiska Time-of-Flight sensorer kan användas för att mäta steghöjd och stegbredd under gång: En utvärdering av sensorer i en laborativ och reell miljö2017Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In some medical cases it is of interest to study a persons gait. This can be done in several different ways, both simple and advanced. A project has been done at the department Medicinsk Teknik - Forskning och Utveckling at the University Hospital of Umeå. In that project a system with optical triangulation sensors was created to easily measure a persons step width and step height. It was found that the sensors had limitations, in particular with sample frequency, and it was therfore of interest to test new sensors for this application. The goal with this project was to evaluate two sensors, VL53L0X and VL6180, and investigate if they can be used to measure step width and step hight. A system was built to communicate with and read data from the sensors. The sensors were then tested both in a laborative and real environment. With good reflection both VL6180 and VL53L0X show good precision in the range of interest. The sensors has the resolution of millimeters. VL6180 works better at really close distances but has a much shorter maximum range, about 18 cm, and lower maximum sample frequency, under 43 Hz. VL53L0X was tested up to 70 cm and 50 Hz. To be able to measure step width from the ankle, a very high sample frequency is needed to get the right amount of data when the legs pass eachother. If the sensors can be used in that way has not been confirmed. When placed higher on the persons leg, VL6180 can be used to measure step width and VL53L0X can be used to measure both step width and step height. 

  • 49.
    Edström, Linnéa
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Armbandsbaserad pulsoximetri: Ett egenkonstruerat system med reflekterande teknik och jämförelse mot traditionell mätteknik vid normal och nedsatt hudtemperatur2016Independent thesis Basic level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In this report a low-cost, portable and wearable design of a new system with reflective technologyfor pulse oximetry is presented. The work has been executed as a project, including electronics construction, software development, a design of the embedding for the prototype and continuous tests of both the hardware and software during the work in progress.

    The result of this work is a prototype system for pulse oximetry. The system can communicate through Bluetooth wireless interface with a PC, laptop or smartphone which supports Bluetooth 4.0. The measurements are shown in real time on a PC/laptop/smartphone. The software is written in mbed with the language C++ for the microprocessor. The project demands different technical skills like signal processing, programming, electronic design and microprocessors. Over all the project is a good introduction for medical technology and a basis for electronic engineers.

    The purpose and goal with the thesis is considered to be reached for the most part and further testing and development of the product is possible.

  • 50.
    Edström, Urban
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics. Centrum för medicinsk teknik och strålningsfysik.
    Nackvinkelmätningar vid thoraxoperation: Kan prismaglasögon underlätta arbetet för operationssjuksköterskor?2017Independent thesis Advanced level (degree of Master (One Year)), 40 credits / 60 HE creditsStudent thesis
12345 1 - 50 of 249
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