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  • 451.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Fast Random Permutation Tests Enable Objective Evaluation of Methods for Single Subject fMRI Analysis2011Inngår i: International Journal of Biomedical Imaging, ISSN 1687-4188, E-ISSN 1687-4196Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Parametric statistical methods, such as Z-, t-, and F-values are traditionally employed in functional magnetic resonance imaging (fMRI) for identifying areas in the brain that are active with a certain degree of statistical significance. These parametric methods, however, have two major drawbacks. First, it is assumed that the observed data are Gaussian distributed and independent; assumptions that generally are not valid for fMRI data. Second, the statistical test distribution can be derived theoretically only for very simple linear detection statistics. With non-parametric statistical methods, the two limitations described above can be overcome. The major drawback of non-parametric methods is the computational burden with processing times ranging from hours to days, which so far have made them impractical for routine use in single subject fMRI analysis. In this work, it is shown how the computational power of cost-efficient Graphics Processing Units (GPUs) can be used to speed up random permutation tests. A test with 10 000 permutations takes less than a minute, making statistical analysis of advanced detection methods in fMRI practically feasible. To exemplify the permutation based approach, brain activity maps generated by the General Linear Model (GLM) and Canonical Correlation Analysis (CCA) are compared at the same significance level. During the development of the routines and writing of the paper, 3-4 years of processing time has been saved by using the GPU.

  • 452.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    fMRI Analysis on the GPU - Possibilities and Challenges2012Inngår i: Computer Methods and Programs in Biomedicine, ISSN 0169-2607, E-ISSN 1872-7565, Vol. 105, nr 2, s. 145-161Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Functional magnetic resonance imaging (fMRI) makes it possible to non-invasively measure brain activity with high spatial resolution.There are however a number of issues that have to be addressed. One is the large amount of spatio-temporal data that needsto be processed. In addition to the statistical analysis itself, several preprocessing steps, such as slice timing correction and motioncompensation, are normally applied. The high computational power of modern graphic cards has already successfully been used forMRI and fMRI. Going beyond the first published demonstration of GPU-based analysis of fMRI data, all the preprocessing stepsand two statistical approaches, the general linear model (GLM) and canonical correlation analysis (CCA), have been implementedon a GPU. For an fMRI dataset of typical size (80 volumes with 64 x 64 x 22 voxels), all the preprocessing takes about 0.5 s on theGPU, compared to 5 s with an optimized CPU implementation and 120 s with the commonly used statistical parametric mapping(SPM) software. A random permutation test with 10 000 permutations, with smoothing in each permutation, takes about 50 s ifthree GPUs are used, compared to 0.5 - 2.5 h with an optimized CPU implementation. The presented work will save time forresearchers and clinicians in their daily work and enables the use of more advanced analysis, such as non-parametric statistics, bothfor conventional fMRI and for real-time fMRI.

  • 453.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Improving CCA based fMRI Analysis by Covariance Pooling - Using the GPU for Statistical Inference2011Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Canonical correlation analysis (CCA) is a statistical methodthat can be preferable to the general linear model (GLM) for analysisof functional magnetic resonance imaging (fMRI) data. There are,however, two problems with CCA based fMRI analysis. First, it is notfeasible to use a parametric approach to calculate an activity thresholdfor a certain signi cance level. Second, two covariance matrices need tobe estimated in each voxel, from a rather small number of time samples.We recently solved the rst problem by doing random permutation testson the graphics processing unit (GPU), such that the null distribution ofany maximum test statistics can be estimated in the order of minutes. Inthis paper we consider the second problem. We extend the idea of variancepooling, that previously has been used for the GLM, to covariancepooling to improve the estimates of the covariance matrices. Our GPUimplementation of random permutation tests is used to calculate signicance thresholds, which are needed to compare the di erent activitymaps in an objective way. The covariance pooling results in more robustestimates of the covariance matrices. The number of signi cantly activevoxels that are detected (thresholded at p = 0.05, corrected for multiplecomparisons) is increased with 40 - 120% (if 8 mm smoothing is appliedto the covariance estimates). Too much covariance pooling can howeverresult in a loss of small activity clusters, 7-10 mm of smoothing givesthe best results. The calculations that were made in order to generatethe results in this paper would have taken a total of about 65 days witha Matlab implementation and about 10 days with a multithreaded Cimplementation, with our multi-GPU implementation they took about 2hours. By using fast random permutation tests, suggested improvementsof existing methods for fMRI analysis can be evaluated in an objective way.

  • 454.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    On Structural Based Certainty for Robust fMRI AnalysisManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    We present a method for obtaining and using a structural based certainty for robust functional magnetic resonance imaging (fMRI) analysis. In the area of fMRI it is common to see brain activity maps with activity at the edge of the brain. It is however a known fact that activity close to the edge of the brain can be due to head movement, since the voxels close to the edge will have a higher variance if they switch between being outside and inside the brain. To some extent this can be remedied by aligning each volume to a reference volume, by the means of volume registration. However, the problem with fMRI volumes is that the slices in the volume normally are taken at different timepoints, and motion between the slices can occur. We calculate a structural based certainty for each voxel, from a high resolution T1-weighted volume, and incorporate this certainty into the statistical analysis of the fMRI data. We show that our certainty approach removes a lot of false activity, both on simulated data and on real data.

  • 455.
    Eklund, Anders
    et al.
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Phase Based Volume Registration Using CUDA2010Inngår i: Acoustics Speech and Signal Processing (ICASSP), 2010, IEEE , 2010, s. 658-661Konferansepaper (Fagfellevurdert)
    Abstract [en]

    We present a method for fast phase based registration of volume data for medical applications. As the number of different modalities within medical imaging increases, it becomes more and more important with registration that works for a mixture of modalities. For these applications the phase based registration approach has proven to be superior. Today there seem to be two kinds of groups that work with medical image registration, one that works with refining of the registration algorithms and one that works with implementation of more simple algorithms on graphic cards for speeding up the algorithms. We put the work from these groups together and get the best from both worlds. We achieve a speedup of 10-30 compared to our CPU implementation, which makes fast phase based registration possible for large medical volumes.

  • 456.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    True 4D Image Denoising on the GPU2011Inngår i: International Journal of Biomedical Imaging, ISSN 1687-4188, E-ISSN 1687-4196, Vol. 2011Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The use of image denoising techniques is an important part of many medical imaging applications. One common application isto improve the image quality of low-dose, i.e. noisy, computed tomography (CT) data. The medical imaging domain has seen atremendous development during the last decades. It is now possible to collect time resolved volumes, i.e. 4D data, with a number ofmodalities (e.g. ultrasound (US), CT, magnetic resonance imaging (MRI)). While 3D image denoising previously has been appliedto several volumes independently, there has not been much work done on true 4D image denoising, where the algorithm considersseveral volumes at the same time (and not a single volume at a time). By using all the dimensions, it is for example possibleto remove some of the time varying reconstruction artefacts that exist in CT volumes. The problem with 4D image denoising,compared to 2D and 3D denoising, is that the computational complexity increases exponentially.In this paper we describe a novel algorithm for true 4D image denoising, based on local adaptive filtering, and how to implementit on the graphics processing unit (GPU). The algorithm was applied to a 4D CT heart dataset of the resolution 512 x 512 x 445 x 20.The result is that the GPU can complete the denoising in about 25 minutes if spatial filtering is used and in about 8 minutes if FFTbased filtering is used. The CPU implementation requires several days of processing time for spatial filtering and about 50 minutesfor FFT based filtering. Fast spatial filtering makes it possible to apply the denoising algorithm to larger datasets (compared to ifFFT based filtering is used). The short processing time increases the clinical value of true 4D image denoising significantly.

  • 457.
    Eklund, Anders
    et al.
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Ohlsson, Henrik
    Linköpings universitet, Institutionen för systemteknik, Reglerteknik. Linköpings universitet, Tekniska högskolan.
    Ynnerman, Anders
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för teknik och naturvetenskap, Visuell informationsteknologi och applikationer. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    A Brain Computer Interface for Communication Using Real-Time fMRI2010Inngår i: Proceedings of the 20th International Conference on Pattern Recognition, Los Alamitos, CA, USA: IEEE Computer Society, 2010, s. 3665-3669Konferansepaper (Fagfellevurdert)
    Abstract [en]

    We present the first step towards a brain computer interface (BCI) for communication using real-time functional magnetic resonance imaging (fMRI). The subject in the MR scanner sees a virtual keyboard and steers a cursor to select different letters that can be combined to create words. The cursor is moved to the left by activating the left hand, to the right by activating the right hand, down by activating the left toes and up by activating the right toes. To select a letter, the subject simply rests for a number of seconds. We can thus communicate with the subject in the scanner by for example showing questions that the subject can answer. Similar BCI for communication have been made with electroencephalography (EEG). The subject then focuses on a letter while different rows and columns of the virtual keyboard are flashing and the system tries to detect if the correct letter is flashing or not. In our setup we instead classify the brain activity. Our system is neither limited to a communication interface, but can be used for any interface where five degrees of freedom is necessary.

  • 458.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Warntjes, Marcel
    Linköpings universitet, Institutionen för medicin och hälsa, Klinisk fysiologi. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Hjärt- och Medicincentrum, Fysiologiska kliniken US.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Phase Based Volume Registration on the GPU with Application to Quantitative MRI2010Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    We present a method for fast phase based registration of volume data for medical applications. As the number of different modalities within medical imaging increases, it becomes more and more important with registration that works for a mixture of modalities. For these applications the phase based registration approach has proven to be superior. Today there seem to be two kinds of groups that work with medical image registration, one that works with refining of the registration algorithms and one that works with implementation of more simple algorithms on graphic cards for speeding up the algorithms. We put the work from these groups together and get the best from both worlds. We achieve a speedup of 10-30 compared to our CPU implementation, which makes fast phase based registration possible for large medical volumes.

  • 459.
    Eklund, Anders
    et al.
    Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, USA.
    Dufort, Paul
    Department of Medical Imaging, University of Toronto, Toronto, Canada.
    Forsberg, Daniel
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    LaConte, Stephen
    Virginia Tech Carilion Research Institute, Virginia Tech, Roanoke, USA.
    Medical Image Processing on the GPU: Past, Present and Future2013Inngår i: Medical Image Analysis, ISSN 1361-8415, E-ISSN 1361-8423, Vol. 17, nr 8, s. 1073-1094Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Graphics processing units (GPUs) are used today in a wide range of applications, mainly because they can dramatically accelerate parallel computing, are affordable and energy efficient. In the field of medical imaging, GPUs are in some cases crucial for enabling practical use of computationally demanding algorithms. This review presents the past and present work on GPU accelerated medical image processing, and is meant to serve as an overview and introduction to existing GPU implementations. The review covers GPU acceleration of basic image processing operations (filtering, interpolation, histogram estimation and distance transforms), the most commonly used algorithms in medical imaging (image registration, image segmentation and image denoising) and algorithms that are specific to individual modalities (CT, PET, SPECT, MRI, fMRI, DTI, ultrasound, optical imaging and microscopy). The review ends by highlighting some future possibilities and challenges.

  • 460.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Forsberg, Daniel
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Using the Local Phase of the Magnitude of the Local Structure Tensor for Image Registration2011Inngår i: Image Analysis: 17th Scandinavian Conference, SCIA 2011, Ystad, Sweden, May 2011. Proceedings / [ed] Anders Heyden, Fredrik Kahl, Springer Berlin/Heidelberg, 2011, Vol. 6688, s. 414-423Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The need of image registration is increasing, especially in the medical image domain. The simplest kind of image registration is to match two images that have similar intensity. More advanced cases include the problem of registering images of different intensity, for which phase based algorithms have proven to be superior. In some cases the phase based registration will fail as well, for instance when the images to be registered do not only differ in intensity but also in local phase. This is the case if a dark circle in the reference image is a bright circle in the source image. While rigid registration algorithms can use other parts of the image to calculate the global transformation, this problem is harder to solve for non-rigid registration. The solution that we propose in this work is to use the local phase of the magnitude of the local structure tensor, instead of the local phase of the image intensity. By doing this, we achieve invariance both to the image intensity and to the local phase and thereby only use the structural information, i.e. the shapes of the objects, for registration.

  • 461.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Friman, Ola
    Fraunhofer Mevis, Bremen, Germany.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    A GPU accelerated interactive interface for exploratory functional connectivity analysis of FMRI data2011Inngår i: Image Processing (ICIP), 2011, IEEE , 2011, s. 1589-1592Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Functional connectivity analysis is a way to investigate how different parts of the brain are connected and interact. A common measure of connectivity is the temporal correlation between a reference voxel time series and all the other time series in a functional MRI data set. An fMRI data set generally contains more than 20,000 within-brain voxels, making a complete correlation analysis between all possible combinations of voxels heavy to compute, store, visualize and explore. In this paper, a GPU-accelerated interactive tool for investigating functional connectivity in fMRI data is presented. A reference voxel can be moved by the user and the correlations to all other voxels are calculated in real-time using the graphics processing unit (GPU). The resulting correlation map is updated in real-time and visualized as a 3D volume rendering together with a high resolution anatomical volume. This tool greatly facilitates the search for interesting connectivity patterns in the brain.

  • 462.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Friman, Ola
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Comparing fMRI Activity Maps from GLM and CCA at the Same Significance Level by Fast Random Permutation Tests on the GPU2011Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Parametric statistical methods are traditionally employed in functional magnetic resonance imaging (fMRI) for identifying areas in the brain that are active with a certain degree of statistical significance. These parametric methods, however, have two major drawbacks. First, it isassumed that the observed data are Gaussian distributed and independent; assumptions that generally are not valid for fMRI data. Second, the statistical test distribution can be derived theoretically only for very simple linear detection statistics. In this work it is shown how the computational power of the Graphics Processing Unit (GPU) can be used to speedup non-parametric tests, such as random permutation tests. With random permutation tests it is possible to calculate significance thresholds for any test statistics. As an example, fMRI activity maps from the General Linear Model (GLM) and Canonical Correlation Analysis (CCA) are compared at the same significance level.

  • 463.
    Eklund, Anders
    et al.
    Virginia Tech, Carilion Research Institute, USA.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Multivariate fMRI Analysis using Canonical Correlation Analysis instead of Classifiers, Comment on Todd et al2013Inngår i: figshare.comArtikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Multivariate pattern analysis (MVPA) is a popular method for making inference about functional magnetic resonance imaging (fMRI) data. One approach is to train a classifier with voxels within a certain radius from the center voxel, to classify between different brain states. This approach is commonly known as the searchlight algorithm. As recently pointed out by Todd and colleagues, inference at the group level can however be confounded by the fact that the direction of the effect is lost if the per subject classification performance is used to generate group results. Here we show that canonical correlation analysis (CCA) can in some aspects be a better approach to multivariate fMRI analysis, than classification based analysis (CBA).

  • 464.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Avdelningen för medicinsk teknik. Linköpings universitet, Institutionen för datavetenskap, Statistik och maskininlärning. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Avdelningen för medicinsk teknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Reply to Chen et al.: Parametric methods for cluster inference perform worse for two‐sided t‐tests2019Inngår i: Human Brain Mapping, ISSN 1065-9471, E-ISSN 1097-0193, Vol. 40, nr 5, s. 1689-1691Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
    Abstract [en]

    One‐sided t‐tests are commonly used in the neuroimaging field, but two‐sided tests should be the default unless a researcher has a strong reason for using a one‐sided test. Here we extend our previous work on cluster false positive rates, which used one‐sided tests, to two‐sided tests. Briefly, we found that parametric methods perform worse for two‐sided t‐tests, and that nonparametric methods perform equally well for one‐sided and two‐sided tests.

  • 465.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Avdelningen för medicinsk teknik. Linköpings universitet, Institutionen för datavetenskap, Statistik och maskininlärning. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Avdelningen för medicinsk teknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Nichols, Thomas E
    Big Data Institute, University of Oxford, Oxford, United Kingdom, Department of Statistics, University of Warwick, Coventry, United KingdomWellcome Trust Centre for Integrative Neuroimaging (WIN-FMRIB), University of Oxford, Oxford, United Kingdom, .
    Cluster failure revisited: Impact of first level design and physiological noise on cluster false positive rates2019Inngår i: Human Brain Mapping, ISSN 1065-9471, E-ISSN 1097-0193, Vol. 40, nr 7, s. 2017-2032Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Methodological research rarely generates a broad interest, yet our work on the validity of cluster inference methods for functional magnetic resonance imaging (fMRI) created intense discussion on both the minutia of our approach and its implications for the discipline. In the present work, we take on various critiques of our work and further explore the limitations of our original work. We address issues about the particular event‐related designs we used, considering multiple event types and randomization of events between subjects. We consider the lack of validity found with one‐sample permutation (sign flipping) tests, investigating a number of approaches to improve the false positive control of this widely used procedure. We found that the combination of a two‐sided test and cleaning the data using ICA FIX resulted in nominal false positive rates for all data sets, meaning that data cleaning is not only important for resting state fMRI, but also for task fMRI. Finally, we discuss the implications of our work on the fMRI literature as a whole, estimating that at least 10% of the fMRI studies have used the most problematic cluster inference method (p = .01 cluster defining threshold), and how individual studies can be interpreted in light of our findings. These additional results underscore our original conclusions, on the importance of data sharing and thorough evaluation of statistical methods on realistic null data.

  • 466.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Statistik. Linköpings universitet, Institutionen för medicinsk teknik, Avdelningen för medicinsk teknik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Filosofiska fakulteten.
    Lindqvist, Martin A
    Department of Biostatistics, Johns Hopkins University, Baltimore, USA.
    Villani, Mattias
    Linköpings universitet, Institutionen för datavetenskap, Statistik. Linköpings universitet, Filosofiska fakulteten.
    A Bayesian Heteroscedastic GLM with Application to fMRI Data with Motion Spikes2017Inngår i: NeuroImage, ISSN 1053-8119, E-ISSN 1095-9572, Vol. 155, s. 354-369Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We propose a voxel-wise general linear model with autoregressive noise and heteroscedastic noise innovations (GLMH) for analyzing functional magnetic resonance imaging (fMRI) data. The model is analyzed from a Bayesian perspective and has the benefit of automatically down-weighting time points close to motion spikes in a data-driven manner. We develop a highly efficient Markov Chain Monte Carlo (MCMC) algorithm that allows for Bayesian variable selection among the regressors to model both the mean (i.e., the design matrix) and variance. This makes it possible to include a broad range of explanatory variables in both the mean and variance (e.g., time trends, activation stimuli, head motion parameters and their temporal derivatives), and to compute the posterior probability of inclusion from the MCMC output. Variable selection is also applied to the lags in the autoregressive noise process, making it possible to infer the lag order from the data simultaneously with all other model parameters. We use both simulated data and real fMRI data from OpenfMRI to illustrate the importance of proper modeling of heteroscedasticity in fMRI data analysis. Our results show that the GLMH tends to detect more brain activity, compared to its homoscedastic counterpart, by allowing the variance to change over time depending on the degree of head motion.

  • 467.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Avdelningen för medicinsk teknik. Linköpings universitet, Institutionen för datavetenskap, Statistik och maskininlärning. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Nichols, Thomas
    University of Warwick, England.
    How open science revealed false positives in brain imaging2017Inngår i: Significance, ISSN 1740-9705, E-ISSN 1740-9713Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
    Abstract [en]

    A team set out to validate software used in fMRI analysis, but ended up invalidating one of neuroscience's most common testing procedures.

  • 468.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för datavetenskap, Statistik.
    Nichols, Thomas
    Department of Statistics, University of Warwick, England.
    Andersson, Mats
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska fakulteten.
    Knutsson, Hans
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska fakulteten.
    Empirically Investigating the Statistical Validity of SPM, FSL and AFNI for Single Subject fMRI Analysis2015Inngår i: 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI), IEEE conference proceedings, 2015, s. 1376-1380Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The software packages SPM, FSL and AFNI are the most widely used packages for the analysis of functional magnetic resonance imaging (fMRI) data. Despite this fact, the validity of the statistical methods has only been tested using simulated data. By analyzing resting state fMRI data (which should not contain specific forms of brain activity) from 396 healthy con- trols, we here show that all three software packages give in- flated false positive rates (4%-96% compared to the expected 5%). We isolate the sources of these problems and find that SPM mainly suffers from a too simple noise model, while FSL underestimates the spatial smoothness. These results highlight the need of validating the statistical methods being used for fMRI. 

  • 469.
    Eklund, Anders
    et al.
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Institutionen för datavetenskap, Statistik. Linköpings universitet, Tekniska fakulteten.
    Nichols, Thomas
    University of Warwick, England.
    Knutsson, Hans
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska fakulteten.
    Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates2016Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, nr 28, s. 7900-7905Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The most widely used task functional magnetic resonance imaging (fMRI) analyses use parametric statistical methods that depend on a variety of assumptions. In this work, we use real resting-state data and a total of 3 million random task group analyses to compute empirical familywise error rates for the fMRI software packages SPM, FSL, and AFNI, as well as a nonparametric permutation method. For a nominal familywise error rate of 5%, the parametric statistical methods are shown to be conservative for voxelwise inference and invalid for clusterwise inference. Our results suggest that the principal cause of the invalid cluster inferences is spatial autocorrelation functions that do not follow the assumed Gaussian shape. By comparison, the nonparametric permutation test is found to produce nominal results for voxelwise as well as clusterwise inference. These findings speak to the need of validating the statistical methods being used in the field of neuroimaging.

  • 470.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Avdelningen för medicinsk teknik. Linköpings universitet, Institutionen för datavetenskap, Statistik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Nichols, Thomas
    Department of Statistics, University of Warwick, UK; WMG, University of Warwick, UK.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Avdelningen för medicinsk teknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Reply to BROWN AND BEHRMANN, COX ET AL., AND KESSLER ET AL.: Data and code sharing is the way forward for fMRI2017Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, s. 1-2Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    We are glad that our paper (1) has generated intense discussions in the fMRI field (2⇓–4), on how to analyze fMRI data, and how to correct for multiple comparisons. The goal of the paper was not to disparage any specific fMRI software, but to point out that parametric statistical methods are based on a number of assumptions that are not always valid for fMRI data, and that nonparametric statistical methods (5) are a good alternative. Through AFNI’s introduction of nonparametric statistics in the function 3dttest++ (3, 6), the three most common fMRI softwares now all support nonparametric group inference [SPM through the toolbox SnPM (www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/nichols/software/snpm), and FSL through the function randomise].

    Cox et al. (3) correctly point out that the bug in the AFNI function 3dClustSim only had a minor impact on the false-positive rate (FPR). This was also covered in our original paper (1): “We note that FWE [familywise error] rates are lower with the bug-fixed 3dClustSim function. As an example, the updated function reduces the degree of false …

  • 471.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Ohlsson, Henrik
    Linköpings universitet, Institutionen för systemteknik, Elektroniksystem. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Rydell, Joakim
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Balancing an Inverted Pendulum by Thinking A Real-Time fMRI Approach2009Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    We present a method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverse pendulum by activating the left or right hand or resting. The brain activity is classified each second by a neural network and the classification is sent to a pendulum simulator to change the force applied to the pendulum. The state of the inverse pendulum is shown to the subject in a pair of VR goggles. The subject was able to balance the inverse pendulum both with real activity and imagined activity. The developments here have a potential to aid people with communication disabilities e.g., locked in people. It might also be a tool for stroke patients to be ableto train the damaged brain area and get real-time feedback of when they do it right.

  • 472.
    Eklund, Anders
    et al.
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Ohlsson, Henrik
    Linköpings universitet, Institutionen för systemteknik, Reglerteknik. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Rydell, Joakim
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Ynnerman, Anders
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för teknik och naturvetenskap, Visuell informationsteknologi och applikationer. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Using Real-Time fMRI to Control a Dynamical System2009Inngår i: ISMRM 17th Scientific Meeting & Exhibition, 2009Konferansepaper (Fagfellevurdert)
    Abstract [en]

    We present e method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverse pendulum by activating the left or right hand or resting. The brain activity is clasified each second by a neural network and the classification is sent to a pendulum simulator to change the state of the pendulum. The state of the inverse pendulum is shown to the subject in a pair of VR goggles. The subject was able to balance the inverse pendulum during a 7 minute test run.

  • 473.
    Eklund, Anders
    et al.
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Ohlsson, Henrik
    Linköpings universitet, Institutionen för systemteknik, Reglerteknik. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Rydell, Joakim
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Ynnerman, Anders
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för teknik och naturvetenskap, Visuell informationsteknologi och applikationer. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Using Real-Time fMRI to Control a Dynamical System2009Rapport (Annet vitenskapelig)
    Abstract [en]

    We present e method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverse pendulum by activating the left or right hand or resting. The brain activity is clasified each second by a neural network and the classification is sent to a pendulum simulator to change the state of the pendulum. The state of the inverse pendulum is shown to the subject in a pair of VR goggles. The subject was able to balance the inverse pendulum during a 7 minute test run.

  • 474.
    Eklund, Anders
    et al.
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Ohlsson, Henrik
    Linköpings universitet, Institutionen för systemteknik, Reglerteknik. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Rydell, Joakim
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Ynnerman, Anders
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Using Real-Time fMRI to Control a Dynamical System by Brain Activity Classification2010Rapport (Annet vitenskapelig)
    Abstract [en]

    We present a method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverted pendulum by activating the left or right hand or resting. The brain activity is classified each second by a neural network and the classification is sent to a pendulum simulator to change the force applied to the pendulum. The state of the inverted pendulum is shown to the subject in a pair of VR goggles. The subject was able to balance the inverted pendulum during several minutes, both with real activity and imagined activity. In each classification 9000 brain voxels were used and the response time for the system to detect a change of activity was on average 2-4 seconds. The developments here have a potential to aid people with communication disabilities, such as locked in people. Another future potential application can be to serve as a tool for stroke and Parkinson patients to be able to train the damaged brain area and get real-time feedback for more efficient training.

  • 475.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Ohlsson, Henrik
    Linköpings universitet, Institutionen för systemteknik, Reglerteknik. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Rydell, Joakim
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Ynnerman, Anders
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Institutionen för teknik och naturvetenskap, Visuell informationsteknologi och applikationer. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Using Real-Time fMRI to Control a Dynamical System by Brain Activity Classification2009Inngår i: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009: 12th International Conference, London, UK, September 20-24, 2009, Proceedings, Part I / [ed] Gerhard Goos, Juris Hartmanis and Jan van Leeuwen, Springer Berlin/Heidelberg, 2009, 1, s. 1000-1008Konferansepaper (Fagfellevurdert)
    Abstract [en]

    We present a method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverted pendulum by activating the left or right hand or resting. The brain activity is classified each second by a neural network and the classification is sent to a pendulum simulator to change the force applied to the pendulum. The state of the inverted pendulum is shown to the subject in a pair of VR goggles. The subject was able to balance the inverted pendulum during several minutes, both with real activity and imagined activity. In each classification 9000 brain voxels were used and the response time for the system to detect a change of activity was on average 2-4 seconds. The developments here have a potential to aid people with communication disabilities, such as locked in people. Another future potential application can be to serve as a tool for stroke and Parkinson patients to be able to train the damaged brain area and get real-time feedback for more efficient training.

  • 476.
    Eklund, Anders
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Warntjes, Marcel
    Linköpings universitet, Institutionen för medicin och hälsa, Klinisk fysiologi. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Hjärtcentrum, Fysiologiska kliniken.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Fast Phase Based Registration for Robust Quantitative MRI2010Inngår i: Proceedings of the annual meeting of the International Society for Magnetic Resonance in Medicine (ISMRM 2010), 2010Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Quantitative magnetic resonance imaging has the major advantage that it handles absolute measurements of physical parameters. Quantitative MRI can for example be used to estimate the amount of different tissue types in the brain, but other applications are possible. Parameters such as relaxation rates R1 and R2 and proton density (PD) are independent of MR scanner settings and imperfections and hence are directly representative of the underlying tissue characteristics. Brain tissue quantification is an important aid for diagnosis of neurological diseases, such as multiple sclerosis (MS) and dementia. It is applied to estimate the volume of each tissue type, such as white tissue, grey tissue, myelin and cerebrospinal fluid (CSF). Tissue that deviates from normal values can be found automatically using computer aided diagnosis. In order for the quantification to have a clinical value, both the time in the MR scanner and the time for the data analysis have to be minimized. A challenge in MR quantification is to keep the scan time within clinically acceptable limits. The quantification method that we have used is based on the work by Warntjes et al.

  • 477.
    Elahi, Pegah
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Application of Noise Invalidation Denoising in MRI2012Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    Magnetic Resonance Imaging (MRI) is a common medical imaging tool that have beenused in clinical industry for diagnostic and research purposes. These images are subjectto noises while capturing the data that can eect the image quality and diagnostics.Therefore, improving the quality of the generated images from both resolution andsignal to noise ratio (SNR) perspective is critical. Wavelet based denoising technique isone of the common tools to remove the noise in the MRI images. The noise is eliminatedfrom the detailed coecients of the signal in the wavelet domain. This can be done byapplying thresholding methods. The main task here is to nd an optimal threshold andkeep all the coecients larger than this threshold as the noiseless ones. Noise InvalidationDenoising technique is a method in which the optimal threshold is found by comparingthe noisy signal to a noise signature (function of noise statistics). The original NIDeapproach is developed for one dimensional signals with additive Gaussian noise. In thiswork, the existing NIDe approach has been generalized for applications in MRI imageswith dierent noise distribution. The developed algorithm was tested on simulated datafrom the Brainweb database and compared with the well-known Non Local Mean lteringmethod for MRI. The results indicated better detailed structural preserving forthe NIDe approach on the magnitude data while the signal to noise ratio is compatible.The algorithm shows an important advantageous which is less computational complexitythan the NLM method. On the other hand, the Unbiased NLM technique is combinedwith the proposed technique, it can yield the same structural similarity while the signalto noise ratio is improved.

  • 478.
    Eneling, Martin
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Fysiologisk mätteknik. Linköpings universitet, Tekniska fakulteten.
    Wickström, M
    Linköpings universitet, Institutionen för medicinsk teknik.
    Johansson, Anders
    Linköpings universitet, Institutionen för medicinsk teknik, Fysiologisk mätteknik. Linköpings universitet, Tekniska fakulteten.
    Hult, Peter
    Linköpings universitet, Institutionen för medicinsk teknik, Fysiologisk mätteknik. Linköpings universitet, Tekniska fakulteten.
    Vätternrundan.  Fjärr-registrering av fysiologiska parametrar under idrottsutövning.2006Konferansepaper (Annet vitenskapelig)
  • 479.
    Engvall, Jan
    et al.
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för kardiovaskulär medicin. Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Östergötlands Läns Landsting, Hjärt- och Medicincentrum, Fysiologiska kliniken US.
    Ask, Per
    Linköpings universitet, Institutionen för medicinsk teknik, Fysiologisk mätteknik. Linköpings universitet, Tekniska högskolan.
    Loyd, Dan
    Linköpings universitet, Institutionen för ekonomisk och industriell utveckling, Mekanisk värmeteori och strömningslära. Linköpings universitet, Tekniska högskolan.
    Wranne, Bengt
    Linköpings universitet, Institutionen för medicin och vård, Klinisk fysiologi. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Hjärt- och Medicincentrum, Fysiologiska kliniken US.
    Coarctation of the aorta--a theoretical and experimental analysis of the effects of a centrally located arterial stenosis.1991Inngår i: Medical and Biological Engineering and Computing, ISSN 0140-0118, E-ISSN 1741-0444, Vol. 29, nr 3, s. 291-296Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aortic coarctation is a local constriction of the aorta that may severely affect haemodynamics. It is therefore important to quantify these effects. Using Bernoulli's equation and the momentum theorem, the pressure drop is described including the pressure recovery distal to the coarctation and the effects of collateral flow; both laminar and turbulent. Assuming the coarctation and collaterals to be stiff, a quadratic relationship between flow and pressure drop is expected for flow through the coarctation and for turbulent collateral flow. For laminar collateral flow, a linear relationship is expected. The coarctation flow was studied in a model consisting of a rigid tube with local constriction, connected to a flooded-level tank, containing a 36 per cent by weight solution of sucrose, with a viscosity equivalent to that of blood at body temperature. The pressure drop across the constriction showed a quadratic relationship to flow in agreement with theoretical expectations. Pressure recovery in this model was very slight (0-4 mm Hg). Nine patients with aortic coarctation were catheterised. Cardiac output and pressure drop across the coarctation were measured at rest and during supine cycle exercise at two different workloads. The relationship between mean pressure drop and cardiac output tended to be either 'parabolic' or, in some cases, approximately linear, suggesting that the flow situation in aortic coarctation can be quantified by expressions that either linearly or quadratically relate pressure and flow.

  • 480.
    Engvall, Jan
    et al.
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för medicin och vård, Klinisk fysiologi. Östergötlands Läns Landsting, Hjärtcentrum, Fysiologiska kliniken.
    Karlsson, Matts
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk modellering och simulering.
    Ask, Per
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Fysiologisk mätteknik.
    Loyd, Dan
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för konstruktions- och produktionsteknik, Mekanisk värmeteori och strömningslära.
    Nylander, Eva
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för medicin och vård, Klinisk fysiologi. Östergötlands Läns Landsting, Hjärtcentrum, Fysiologiska kliniken.
    Wranne, Bengt
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för medicin och vård, Klinisk fysiologi. Östergötlands Läns Landsting, Hjärtcentrum, Fysiologiska kliniken.
    Importance of collateral vessels in aortic coarctation: Computer simulation at rest and exercise using transmission line elements1994Inngår i: Medical & Biological Engineering & Computing, ISSN 0140-0118, Vol. 32, s. 115-122Artikkel i tidsskrift (Fagfellevurdert)
  • 481.
    Enlund, Gunnar
    et al.
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för medicin och vård, Anestesiologi. Östergötlands Läns Landsting, Anestesi- och operationscentrum, Intensivvårdskliniken US.
    Johansson, M
    Vegfors, Magnus
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för medicin och vård, Anestesiologi. Östergötlands Läns Landsting, Anestesi- och operationscentrum, Anestesi- och intensivvårdskliniken VIN.
    Lindberg, Lars-Göran
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Fysiologisk mätteknik.
    Photoplethysmography (PPG) reflexts changes in blood flow at different vascular levels1997Inngår i: World Congress on Medical Physics and Biomedical Engineering,1997, 1997Konferansepaper (Fagfellevurdert)
  • 482.
    Eriksson Bylund, Nina
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Ressner, Marcus
    Linköpings universitet, Institutionen för medicinsk teknik, Fysiologisk mätteknik. Linköpings universitet, Tekniska högskolan.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    3D Wiener filtering to reduce reverberations in ultrasound image sequences2003Inngår i: Image Analysis: 13th Scandinavian Conference, SCIA 2003 Halmstad, Sweden, June 29 – July 2, 2003 Proceedings / [ed] Josef Bigun and Tomas Gustavsson, Springer, 2003, Vol. 2749, s. 579-586Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    One of the most frequently occuring artifacts in ultrasound imaging is reverberations. These are multiple reflection echoes that result in ghost echoes in the ultrasound image. A method for reducing these unwanted artifacts using a three-dimensional (3D) Wiener filter is presented. The Wiener filter is a global filter and produces an estimate of the uncorrupted signal by minimizing the mean square error between the estimate and the uncorrupted signal in a statistical sense. The procedure works as follows: In a graphic interface the operator is displayed an image sequence. The operator marks two areas in one of the images, one area which contains a typical reverberation artifact, and one area free from artifact. Using these areas to produce noise and signal estimates, a Wiener filter is created and applied to the sequence. The 3D Wiener filters display excellent selection capabilities, and the developed method significantly reduces the magnitude of the reverberation artifact in the tested sequences.

  • 483.
    Eriksson, Charlotte
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik.
    Optimization of Dual Energy data acquisition using CdTe-detectors with electronic spectrum splitting2013Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    Dual energy imaging has made it possible to enhance contrast in medical images using images containing different energy information, by combining low and high energy images. Dual energy data can either be acquired using double exposures or splitting the energy spectrum into two images using one exposure.

    This thesis presents investigations of dual energy imaging using a detector solution developed by XCounter which provides dual energy images in a single exposure with a threshold separating low and high energy images. Phantom experiments with phantoms of aluminum and plexiglas were performed using weighted logarithmic subtraction and basis material decomposition to produce dual energy images. Methods were validated and images were evaluated in terms of signal difference in noise ratio to find the threshold and tube voltage combination for optimum energy spectrum separation. The methods were also tested on biological materials using bone, soft tissue and iodine solution as contrast enhancer, to investigate K-edge imaging. 

    Optimal separation of plexiglas and aluminum were found at 70 kVp and the threshold parameter set within a range of 8 to 9, which corresponds to approximately 30 to 34 keV. For K-edge imaging, the optimum separation were found close to K-edge energy of iodine. The results found in the phantom study correlated with results from the biological material study.

  • 484. Eriksson, O.
    et al.
    Johansson, Johannes
    Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik. Linköpings universitet, Tekniska högskolan.
    Wårdell, Karin
    Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik. Linköpings universitet, Tekniska högskolan.
    Finite element simulations of rf lesions in porcine brain2002Konferansepaper (Fagfellevurdert)
  • 485.
    Eriksson, Ola
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Characterisation and modelling of radio-frequency lesioning in functional neurosurgery2001Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis focuses on the characterisation and modelling of the radio frequency (RF) lesioning with emphasis on size estimation in functional neurosurgery. A computer-assisted video system has been set up for standardised test and documentation of protein clots generated by RF-lesioning electrodes in an albumin solution. A standardised test is essential in comparing assessed results of the size and shape of protein clots generated using different parameters. This is beneficial to both the manufacturer oflesioning electrodes as well as the surgeon.

    In an animal study, performed analogously to thalamotomy in man, the correlation in size between in vitro protein clots and in vivo lesions has been investigated. The result shows a high correlation between protein clots and lesions observed on MR images; and lesions observed on MR images and corresponding coagulated tissue in histological sectionings. This actualises the value of presurgical electrode tests to validate the electrode function and lesion size in vitro.

    A finite element model has been set-up in order to facilitate studies of the growth and the temperature distribution during the lesioning process. Of the utmost importance is the finding of a difference in temperature between maximum temperature, located outside the electrode, compared to the intra-electrode (thermocouple) temperature.

    A method for real time monitoring of lesion growth and estimation of lesion size utilising static and/or Doppler broadened laser light is proposed. Implemented in a surgical-assist system, this could give valuable guidance to the surgeon as to whether the desired lesion size is obtained or not and keep the destruction precise, but to a minimum.

    Delarbeid
    1. In vitro evaluation of brain lesioning electrodes (Leksell) using a computer-assisted video system
    Åpne denne publikasjonen i ny fane eller vindu >>In vitro evaluation of brain lesioning electrodes (Leksell) using a computer-assisted video system
    Vise andre…
    1999 (engelsk)Inngår i: Neurological Research, ISSN 0161-6412, E-ISSN 1743-1328, Vol. 21, nr 1, s. 89-95Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Radiofrequency (RF) generated thermal brain lesions are widely used in functional neurosurgery. The size, shape and development of the lesions depends on system parameter settings and the electrode configuration. Difficulties in studying the effect of these factors in vivo stimulated us to develop an in vitro system for standardized comparison between different electrodes and physical parameters. A computer-assisted video system was set-up allowing continuous video recording of RF-generated coagulations in either a standard albumin solution or in the fresh white of a hen's egg as transparent test substrates. Ten lesions were made with each test electrode (two bipolar and three monopolar) in each of the two substrates at 70 degrees, 80 degrees and 90 degrees C (t = 60 sec). Due to the better homogeneity the lesions in the albumin solution were much more regular and reproducible. This made it possible to calculate the size (width 2.2 +/- 0.1 to 5.3 +/- 0.1 mm and length 3.0 +/- 0.1 to 8.7 +/- 0.3 mm) as well as the volume (8.5 +/- 1.4 mm3 to 133.5 +/- 26.8 mm3). It is concluded that this in vitro system offers a reproducible way to study and document the effect of different electrode configurations and RF-generator settings on the formation of a heat lesion. Even if the results are not directly applicable to the living human brain they give an estimate of the form and size of a coagulation lesion and can be of value for standardized comparisons between different electrodes.

    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-30203 (URN)10048063 (PubMedID)15697 (Lokal ID)15697 (Arkivnummer)15697 (OAI)
    Tilgjengelig fra: 2009-10-09 Laget: 2009-10-09 Sist oppdatert: 2017-12-13
    2. In-vitro size estimation of protein clots generated by brain electrodes
    Åpne denne publikasjonen i ny fane eller vindu >>In-vitro size estimation of protein clots generated by brain electrodes
    1998 (engelsk)Inngår i: Proceedings of the 20th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 1998 / [ed] H. K. Chang, Y. T. Zhang, Hong Kong: IEEE , 1998, s. 1783-Konferansepaper, Publicerat paper (Fagfellevurdert)
    Abstract [en]

    A method for in-vitro size estimation of protein clots generated by brain electrodes is presented. Radiofrequency generated thermal brain lesions are widely used in functional neurosurgery and in-vitro tests are used to confirm the electrodes' ability to generate lesions. To be able to estimate the size of protein clots generated in-vitro by brain electrodes, a computer-assisted video system was set up. The size estimation is carried out by software using two captured images of the protein clot. The “true” length and width (9.5 mm) of a sphere as measured with a slide-caliper differed at the most 0.5 mm (5%) and 0.3 mm (3%) respectively, all random errors fall within 2s.d

    sted, utgiver, år, opplag, sider
    Hong Kong: IEEE, 1998
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-31111 (URN)10.1109/IEMBS.1998.746933 (DOI)16842 (Lokal ID)16842 (Arkivnummer)16842 (OAI)
    Konferanse
    The 20th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, October 29 - November 1 1998, Hong Kong SAR, China
    Tilgjengelig fra: 2009-10-09 Laget: 2009-10-09 Sist oppdatert: 2016-05-04
    3. Experimental radiofrequency brain lesions: a volumetric study
    Åpne denne publikasjonen i ny fane eller vindu >>Experimental radiofrequency brain lesions: a volumetric study
    Vise andre…
    2002 (engelsk)Inngår i: Neurosurgery, ISSN 0148-396X, E-ISSN 1524-4040, Vol. 51, nr 3, s. 781-788Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    OBJECTIVE : This study describes the production, under strictly standardized and controlled conditions, of radiofrequency lesions with identical neurogenerator settings: in vitro in two different albumin solutions (nongelatinous and gelatinous) and in vivo in the thalamus of the pig.

    METHODS : The radiofrequency lesions were investigated in vitro by the use of a specially designed video system and in vivo by magnetic resonance imaging. Moreover, the size of the in vivo lesions was estimated with the use of histological sectioning. The statistical analysis included the calculation of a correlation coefficient for the length, width, and volume for each lesion estimation.

    RESULTS : A high correlation (R = 0.96, P < 0.005; n = 14) was found between clot sizes in the two albumin solutions. Albumin clots generated in gelatinous albumin showed systematically larger volumes. In the pig, two concentric zones were seen in all magnetic resonance images and all histological preparations. The width correlation of the completely coagulated brain tissue (inner zones) was R = 0.94, P < 0.005, and n = 7. The corresponding correlation between magnetic resonance images and gelatinous albumin was R = 0.93, P < 0.005, and n = 7. As a rule, the in vitro clots were smaller than the outer zone but larger than the inner zone of the magnetic resonance imaging-recorded lesions for all of the electrode and temperature combinations tested. In vivo lesions generated with the same electrode and parameter settings showed high reproducibility.

    CONCLUSION : The value of presurgical electrode tests to validate the electrode function and lesion size in vitro has become evident in this study, which shows a high correlation between the in vitro albumin clots and the in vivo lesions observed on magnetic resonance images.

    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-29944 (URN)10.1097/00006123-200209000-00030 (DOI)15370 (Lokal ID)15370 (Arkivnummer)15370 (OAI)
    Tilgjengelig fra: 2009-10-09 Laget: 2009-10-09 Sist oppdatert: 2017-12-13
    4. A comparison between in vitro studies of protein lesions generated by brain electrodes and finite element model simulations
    Åpne denne publikasjonen i ny fane eller vindu >>A comparison between in vitro studies of protein lesions generated by brain electrodes and finite element model simulations
    1999 (engelsk)Inngår i: Medical and Biological Engineering and Computing, ISSN 0140-0118, E-ISSN 1741-0444, Vol. 37, nr 6, s. 737-741Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The aim of this study was to develop a finite element model for simulation of the thermal characteristics of brain electrodes and to compare its performances with an in vitro experimental albumin model. Ten lesions were created in albumin using a monopolar electrode connected to a Leksell Neuro Generator and a computer-assisted video system was used to determine the size of the generated lesions. A finite element model was set up of the in vitro experiments using the same thermal properties. With a very simple heat source applied to the finite element model in the proximity of the upper part of the tip, a good agreement (no deviations in width and distance from tip but a deviation in length of −1.6 mm) with the in vitro experiments (width 4.6±0.1 mm and length 7.4±0.1 mm) was achieved when comparing the outline of the lesion. In addition, a gelatinous albumin-model was set up and compared to computer simulations resulting in deviations in width of −0.4 mm, length of −2.2 mm and distance from the tip of −0.1 mm. Hence, the utilisation of finite element model simulations may be a useful complement to in-vitro experiments.

    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-30204 (URN)10.1007/BF02513376 (DOI)15698 (Lokal ID)15698 (Arkivnummer)15698 (OAI)
    Tilgjengelig fra: 2009-10-09 Laget: 2009-10-09 Sist oppdatert: 2017-12-13
    5. Analysis of temperature measurement for monitoring radio-frequency brain lesioning
    Åpne denne publikasjonen i ny fane eller vindu >>Analysis of temperature measurement for monitoring radio-frequency brain lesioning
    2001 (engelsk)Inngår i: Medical and Biological Engineering and Computing, ISSN 0140-0118, E-ISSN 1741-0444, Vol. 39, nr 2, s. 255-262Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    During ablative neurosurgery of movement disorders, for instance therapy of Parkinson's disease, temperature monitoring is crucial. This study aims at a quantitative comparison of measurement deviations between the maximum temperature located outside the lesioning electrode and two possible thermocouple locations inside the electrode. In order to obtain the detailed temperature field necessary for the analysis, four finite element models associated with different surroundings and with different power supplies are studied. The results from the simulations show that both the power level and the power density as well as the surrounding medium affect the temperature measurement and the temperature field in general. Since the maximum temperature is located outside the electrode there will always be a deviation in time and level between the measured and the maximum temperature. The deviation is usually 2–7 s and 3–12°C, depending on, for example, the thermocouple location and surrounding medium. Therefore, not only the measured temperature but also the relation between measured and maximum temperature must be accounted for during therapy and device design.

    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-29926 (URN)10.1007/BF02344810 (DOI)15351 (Lokal ID)15351 (Arkivnummer)15351 (OAI)
    Tilgjengelig fra: 2009-10-09 Laget: 2009-10-09 Sist oppdatert: 2017-12-13
    6. Optical changes as a marker for lesion size estimation during radio frequency ablation: a model study
    Åpne denne publikasjonen i ny fane eller vindu >>Optical changes as a marker for lesion size estimation during radio frequency ablation: a model study
    2001 (engelsk)Inngår i: SPIE Proceedings | Volume 4254 | Guidance, Surgical-Assist and Treatment Systems / [ed] Warren S. Grundfest; David A. Benaron; Tuan Vo-Dinh, 2001, Vol. 4254, s. 164-171Konferansepaper, Publicerat paper (Annet vitenskapelig)
    Abstract [en]

    Stereotactic radiofrequency (RF)-lesioning in the central part of the brain is performed on patients that, for instance, have severe movement or psychiatric disorders. The size of the generated lesion can to some extent be controlled by RF-generator settings such as temperature and time as well as the electrode configuration. Today, MR- imaging and CT are the essential diagnostic methods to confirm the lesion size in vivo. The aim of this study was to investigate whether it is possible to use changes in the reflected light intensity and laser Doppler flowmetry as a marker for size estimation during RF-lesioning.

    Emneord
    Brain electrodes, Laser doppler flowmetry, Reflection spectroscopy, RF-lesioning
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-47497 (URN)10.1117/12.427930 (DOI)
    Konferanse
    Biomedical Diagnostic, Guidance, and Surgical-Assist Systems III, San Jose, CA, January 20, 2001
    Tilgjengelig fra: 2009-10-11 Laget: 2009-10-11 Sist oppdatert: 2016-05-04
  • 486.
    Eriksson, Ola
    Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik. Linköpings universitet, Tekniska högskolan.
    Characterisation of brain electrodes for ablative neurosurgery1999Licentiatavhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Stereotactic ablative neurosurgery with radio frequency current is regularly performed on patients with movement disorders, for instance Parkinson's disease. Even though the technique has been used for ablation in the brain for almost 50 years, nobody has suggested a standardised way of testing the electrodes used for ablative surgery.

    Within the framework of this thesis a computer-assisted video system has been developed for a proposed standardised method for in vitro estimation of protein clots generated by radio frequency lesioning electrodes. The system can be used for documentation of lesion growth by video recording, as well as lesion shape and size Oength, width and volume) calculations by use of two perpendicularly captured images of the protein clot. The system has been used for this purpose in a comparative study including two different test solutions (albumin and hen's egg white), three different temperature settings (70, 80 or 90°C) and five different brain electrode configurations, three monopolar (2mm diameter and 4mm tip, 1mm diameter and 2 or 4mm tip) and two bipolar (1 or 2mm diameter). Electrode configurations and parameter settings of the radio frequency generator greatly affect the size and shape of the coagulated lesion. Larger electrodes and higher temperature settings produce larger lesions, while the shape of the lesion is more dependent on the choice between monopolar or bipolar electrodes and the length of the active uninsulated electrode tip. The experiments performed in the albumin solution showed more regular, reproducible and homogeneous shapes and sizes compared to the experiments performed in hen's egg white. Protein clots generated by the electrodes in the albumin solution ranged in width from 2.2±0.1 to 5.3±0.lmm, length from 3.0±0.1 to 8.7±0.3mm and volume from 8.5±1.4 to 133.5±26.8mm3 , (m±s.d.,n=10). By using different test patterns, the video system has been  proven to be accurate and precise (random error 2%), giving repeatable and reproducible results.

    A method for simulation of the thermal characteristics of brain lesioning electrodes using the finite element method has also been developed. Finite element simulations of thein vitro experiment give valuable information of the lesion growth and final size when using different thermal properties and conditions. No deviation in width and distance from tip was seen when comparing finite element simulations of a power distribution at the distal part of the tip to in vitro experiments. However, the length is somewhat underestimated.

    In conclusion, the developed computer-assisted video system can be used as a standard system for evaluation of radio frequency electrodes used in stereotactic ablative neurosurgery. The proposed albumin solution is superior to egg white and should be used as a test substrate. An FEM simulation offers a good approximation for assessment of the size of the in vitro lesion.

  • 487.
    Eriksson, Ola
    et al.
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik.
    Backlund, Erik Olof
    Lindstam, Håkan
    Lundberg, Peter
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för medicin och vård, Medicinsk radiofysik. Östergötlands Läns Landsting, Kirurgi- och onkologicentrum, Radiofysikavdelningen.
    Lindström, Sivert
    Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Institutionen för biomedicin och kirurgi, Avdelningen för medicinsk cellbiologi.
    Wårdell, Karin
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik.
    Stereotactic RF-lesioning - A study in the pig brain2000Inngår i: Scandinavian Neurosurgical Society Meeting,2000, 2000Konferansepaper (Fagfellevurdert)
  • 488.
    Eriksson, Ola
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik. Linköpings universitet, Tekniska högskolan.
    Backlund, Erik-Olof
    Linköpings universitet, Institutionen för nervsystem och rörelseorgan, Neurokirurgi. Linköpings universitet, Hälsouniversitetet.
    Lundberg, Peter
    Linköpings universitet, Institutionen för medicin och vård, Medicinsk radiofysik. Linköpings universitet, Hälsouniversitetet.
    Lindstam, Håkan
    Linköpings universitet, Institutionen för medicin och vård, Radiologi. Linköpings universitet, Hälsouniversitetet.
    Lindström, Sivert
    Linköpings universitet, Institutionen för biomedicin och kirurgi, Cellbiologi. Linköpings universitet, Hälsouniversitetet.
    Wårdell, Karin
    Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik. Linköpings universitet, Tekniska högskolan.
    Experimental radiofrequency brain lesions: a volumetric study2002Inngår i: Neurosurgery, ISSN 0148-396X, E-ISSN 1524-4040, Vol. 51, nr 3, s. 781-788Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    OBJECTIVE : This study describes the production, under strictly standardized and controlled conditions, of radiofrequency lesions with identical neurogenerator settings: in vitro in two different albumin solutions (nongelatinous and gelatinous) and in vivo in the thalamus of the pig.

    METHODS : The radiofrequency lesions were investigated in vitro by the use of a specially designed video system and in vivo by magnetic resonance imaging. Moreover, the size of the in vivo lesions was estimated with the use of histological sectioning. The statistical analysis included the calculation of a correlation coefficient for the length, width, and volume for each lesion estimation.

    RESULTS : A high correlation (R = 0.96, P < 0.005; n = 14) was found between clot sizes in the two albumin solutions. Albumin clots generated in gelatinous albumin showed systematically larger volumes. In the pig, two concentric zones were seen in all magnetic resonance images and all histological preparations. The width correlation of the completely coagulated brain tissue (inner zones) was R = 0.94, P < 0.005, and n = 7. The corresponding correlation between magnetic resonance images and gelatinous albumin was R = 0.93, P < 0.005, and n = 7. As a rule, the in vitro clots were smaller than the outer zone but larger than the inner zone of the magnetic resonance imaging-recorded lesions for all of the electrode and temperature combinations tested. In vivo lesions generated with the same electrode and parameter settings showed high reproducibility.

    CONCLUSION : The value of presurgical electrode tests to validate the electrode function and lesion size in vitro has become evident in this study, which shows a high correlation between the in vitro albumin clots and the in vivo lesions observed on magnetic resonance images.

  • 489.
    Eriksson, Ola
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Wren, Joakim
    Linköpings universitet, Institutionen för konstruktions- och produktionsteknik, Fluid och mekanisk systemteknik. Linköpings universitet, Tekniska högskolan.
    Loyd, Dan
    Linköpings universitet, Institutionen för konstruktions- och produktionsteknik, Fluid och mekanisk systemteknik. Linköpings universitet, Tekniska högskolan.
    Wårdell, Karin
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    A comparison between in vitro studies of protein lesions generated by brain electrodes and finite element model simulations1999Inngår i: Medical and Biological Engineering and Computing, ISSN 0140-0118, E-ISSN 1741-0444, Vol. 37, nr 6, s. 737-741Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The aim of this study was to develop a finite element model for simulation of the thermal characteristics of brain electrodes and to compare its performances with an in vitro experimental albumin model. Ten lesions were created in albumin using a monopolar electrode connected to a Leksell Neuro Generator and a computer-assisted video system was used to determine the size of the generated lesions. A finite element model was set up of the in vitro experiments using the same thermal properties. With a very simple heat source applied to the finite element model in the proximity of the upper part of the tip, a good agreement (no deviations in width and distance from tip but a deviation in length of −1.6 mm) with the in vitro experiments (width 4.6±0.1 mm and length 7.4±0.1 mm) was achieved when comparing the outline of the lesion. In addition, a gelatinous albumin-model was set up and compared to computer simulations resulting in deviations in width of −0.4 mm, length of −2.2 mm and distance from the tip of −0.1 mm. Hence, the utilisation of finite element model simulations may be a useful complement to in-vitro experiments.

  • 490.
    Eriksson, Ola
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Wårdell, Karin
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    In-vitro size estimation of protein clots generated by brain electrodes1998Inngår i: Proceedings of the 20th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 1998 / [ed] H. K. Chang, Y. T. Zhang, Hong Kong: IEEE , 1998, s. 1783-Konferansepaper (Fagfellevurdert)
    Abstract [en]

    A method for in-vitro size estimation of protein clots generated by brain electrodes is presented. Radiofrequency generated thermal brain lesions are widely used in functional neurosurgery and in-vitro tests are used to confirm the electrodes' ability to generate lesions. To be able to estimate the size of protein clots generated in-vitro by brain electrodes, a computer-assisted video system was set up. The size estimation is carried out by software using two captured images of the protein clot. The “true” length and width (9.5 mm) of a sphere as measured with a slide-caliper differed at the most 0.5 mm (5%) and 0.3 mm (3%) respectively, all random errors fall within 2s.d

  • 491.
    Eriksson, Ola
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik. Linköpings universitet, Tekniska högskolan.
    Wårdell, Karin
    Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik. Linköpings universitet, Tekniska högskolan.
    Optical changes as a marker for lesion size estimation during radio frequency ablation: a model study2001Inngår i: SPIE Proceedings | Volume 4254 | Guidance, Surgical-Assist and Treatment Systems / [ed] Warren S. Grundfest; David A. Benaron; Tuan Vo-Dinh, 2001, Vol. 4254, s. 164-171Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Stereotactic radiofrequency (RF)-lesioning in the central part of the brain is performed on patients that, for instance, have severe movement or psychiatric disorders. The size of the generated lesion can to some extent be controlled by RF-generator settings such as temperature and time as well as the electrode configuration. Today, MR- imaging and CT are the essential diagnostic methods to confirm the lesion size in vivo. The aim of this study was to investigate whether it is possible to use changes in the reflected light intensity and laser Doppler flowmetry as a marker for size estimation during RF-lesioning.

  • 492.
    Eriksson, Ola
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Wårdell, Karin
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Eriksson-Bylund, Nina
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Kullberg, Gunvor
    Department of Neurosurgery, University of Lund, Lund, Sweden.
    Rehncrona, Stig
    Department of Neurosurgery, University of Lund, Lund, Sweden.
    In vitro evaluation of brain lesioning electrodes (Leksell) using a computer-assisted video system1999Inngår i: Neurological Research, ISSN 0161-6412, E-ISSN 1743-1328, Vol. 21, nr 1, s. 89-95Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Radiofrequency (RF) generated thermal brain lesions are widely used in functional neurosurgery. The size, shape and development of the lesions depends on system parameter settings and the electrode configuration. Difficulties in studying the effect of these factors in vivo stimulated us to develop an in vitro system for standardized comparison between different electrodes and physical parameters. A computer-assisted video system was set-up allowing continuous video recording of RF-generated coagulations in either a standard albumin solution or in the fresh white of a hen's egg as transparent test substrates. Ten lesions were made with each test electrode (two bipolar and three monopolar) in each of the two substrates at 70 degrees, 80 degrees and 90 degrees C (t = 60 sec). Due to the better homogeneity the lesions in the albumin solution were much more regular and reproducible. This made it possible to calculate the size (width 2.2 +/- 0.1 to 5.3 +/- 0.1 mm and length 3.0 +/- 0.1 to 8.7 +/- 0.3 mm) as well as the volume (8.5 +/- 1.4 mm3 to 133.5 +/- 26.8 mm3). It is concluded that this in vitro system offers a reproducible way to study and document the effect of different electrode configurations and RF-generator settings on the formation of a heat lesion. Even if the results are not directly applicable to the living human brain they give an estimate of the form and size of a coagulation lesion and can be of value for standardized comparisons between different electrodes.

  • 493.
    Eriksson, Ola
    et al.
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik.
    Wårdell, Karin
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik.
    Kullberg, G
    Rehncrona, S
    Invitro evaluation of brain lesioning electrodes (Leksell) using a computer-based video system1997Inngår i: XIIth Meeting World Society Stereotactic Functional Neurosurgery,1997, 1997Konferansepaper (Fagfellevurdert)
  • 494.
    Eriksson, Ola
    et al.
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik.
    Wårdell, Karin
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik.
    Wren, Joakim
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för konstruktions- och produktionsteknik, Mekanisk värmeteori och strömningslära.
    Loyd, Dan
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för konstruktions- och produktionsteknik, Mekanisk värmeteori och strömningslära.
    A finite element model for brain electrodes and its comparison with in-vitro albumin lesions1999Inngår i: Congress of the International Society for Neurosurgical Technology and Instrument Invention ISNTII,1999, 1999Konferansepaper (Annet vitenskapelig)
  • 495.
    Eriksson, Olle
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Statistik. Linköpings universitet, Filosofiska fakulteten.
    Backlund, EO
    Lundberg, Peter
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för radiologiska vetenskaper. Linköpings universitet, Hälsouniversitetet. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Östergötlands Läns Landsting, Centrum för kirurgi, ortopedi och cancervård, Radiofysikavdelningen US.
    Lindstam, H
    Wårdell, Karin
    Linköpings universitet, Institutionen för medicinsk teknik, Biomedicinsk instrumentteknik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    A method for comparisons between in vitro, in vivo and post mortem appearance of tereotactic RF-lesions in the pig brain.2000Konferansepaper (Annet vitenskapelig)
  • 496.
    Eriksson, Stefanie
    et al.
    Lund University, Sweden.
    Lasic, Samo
    CR Dev AB, Sweden.
    Nilsson, Markus
    Lund University, Sweden.
    Westin, Carl-Fredrik
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Harvard University, MA 02215 USA.
    Topgaard, Daniel
    Lund University, Sweden.
    NMR diffusion-encoding with axial symmetry and variable anisotropy: Distinguishing between prolate and oblate microscopic diffusion tensors with unknown orientation distribution2015Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 142, nr 10, s. 104201-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We introduce a nuclear magnetic resonance method for quantifying the shape of axially symmetric microscopic diffusion tensors in terms of a new diffusion anisotropy metric, D-Delta, which has unique values for oblate, spherical, and prolate tensor shapes. The pulse sequence includes a series of equal-amplitude magnetic field gradient pulse pairs, the directions of which are tailored to give an axially symmetric diffusion-encoding tensor b with variable anisotropy b(Delta). Averaging of data acquired for a range of orientations of the symmetry axis of the tensor b renders the method insensitive to the orientation distribution function of the microscopic diffusion tensors. Proof-of-principle experiments are performed on water in polydomain lyotropic liquid crystals with geometries that give rise to microscopic diffusion tensors with oblate, spherical, and prolate shapes. The method could be useful for characterizing the geometry of fluid-filled compartments in porous solids, soft matter, and biological tissues. (C) 2015 Author(s).

  • 497.
    Eriksson-Bylund, Nina
    Linköpings universitet, Institutionen för medicinsk teknik. Linköpings universitet, Tekniska högskolan.
    Spatio-temporal filtering of ultrasound image sequences2004Licentiatavhandling, monografi (Annet vitenskapelig)
    Abstract [en]

    A number of diseases result in reduced perfusion of the vital organs of the body. Measures of the blood flow in the small vessels (the perfusion) of these organs would contribute significantly to a clinical diagnosis. Myocardial contrast echocardiography is a rapidly developing technique for non-invasive ultrasound imaging of perfusion. The work presented in this thesis is related to the preprocessing of the ultrasound data in order to facilitate the segmentation of the heart walls in which the perfusion is to be estimated.

    In an ultrasound image artifacts can occur for a number of reasons. These lead to a more complicated interpretation procedure as important information may be obscured or lost. One of the most frequently occuring artifacts in diagnostic ultrasound imaging is reverberation. This type of artifact is caused by the incorrect assumption that the ultrasound pulse's propagation path is always straight to a backscattering target and straight back to the transducer. Reverberation artifacts may be seen as multiple ghost structures in the ultrasound image.

    A method to detect these reverberation artifacts has been developed and tested on three different ultrasound image sequences. The method uses ratios of lognormal quadrature filter responses to estimate the local bandwidth of the ultrasound signal. For the in-vivo sequences the result is a "map" indicating the artifact locations.

    In order to reduce the reverberation artifacts an interactive procedure for estimating two­ dimensional and three-dimensional Wiener filters has been developed. The design procedure used is a weighted least squares approach, in which both a frequency and a spatiotemporal weighting function are used to optimize the filter. In the results after filtering with the optimized filters the magnitude of the artifact is significantly reduced. For the in-vivo sequences the 3D approach display a better selection capability compared to the 2D approach.

    The results from these studies show that the proposed methods constitute a promising basis for a useful clinical tool.

  • 498.
    Eriksson-Bylund, Nina
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Detecting and reducing reverberation artifacts2004Inngår i: Proceedings of the Swedish Symposium on Image Analysis (2004), 2004, s. 54-57Konferansepaper (Annet vitenskapelig)
  • 499.
    Eriksson-Bylund, Nina
    et al.
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan.
    Andersson, Mats
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Knutsson, Hans
    Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik. Linköpings universitet, Tekniska högskolan. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Interactive 3D filter design for ultrasound artifact reduction2005Inngår i: Image Processing, 2005. ICIP 2005. IEEE International Conference on  (Volume:3 ), 2005, s. 728-731Konferansepaper (Fagfellevurdert)
    Abstract [en]

    A method for detecting and reducing reverberation artifacts in ultrasound image sequences is described. A reverberation artifact localization map is produced using local Rf-bandwidth estimation. To reduce the artifacts an ideal 3D (2D + time) Wiener filter function is computed by using the reverberation map to interactively produce an estimate of the noise and signal spectra. The Wiener filter kernel is optimized to obtain good locality properties. The optimized filter is then applied to the ultrasound image sequence. The test sequence used is from an open chest pig heart, corrupted by strong reverberation artifacts. The selective power of a 3D filter is far superior to that of ID and 2D filters and the reverberation artifacts are almost completely removed by the developed method.

  • 500.
    Eriksson-Bylund, Nina
    et al.
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Andersson, Mats
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Knutsson, Hans
    Linköpings universitet, Tekniska högskolan. Linköpings universitet, Institutionen för medicinsk teknik, Medicinsk informatik.
    Wide range frequensy estimation in ultrasound images2001Inngår i: SSAB Symposium on Image Analysis,2001, 2001Konferansepaper (Annet vitenskapelig)
78910111213 451 - 500 of 2206
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