| 1. |
- Fritzell, Peter, et al.
(författare)
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Bacteria : back pain, leg pain and Modic sign—a surgical multicentre comparative study
- 2019
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Ingår i: European spine journal. - : Springer. - 0940-6719 .- 1432-0932. ; 28:12, s. 2981-2989
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To compare bacterial findings in pain-generating degenerated discs in adults operated on for lumbar disc herniation (LDH), and mostly also suffering from low back pain (LBP), with findings in adolescent patients with non-degenerated non-pain-generating discs operated on for scoliosis, and to evaluate associations with Modic signs on magnetic resonance imaging (MRI). Cutibacterium acnes (Propionibacterium acnes) has been found in painful degenerated discs, why it has been suggested treating patients with LDH/LBP with antibiotics. As multidrug-resistant bacteria are a worldwide concern, new indications for using antibiotics should be based on solid scientific evidence.Methods: Between 2015 and 2017, 40 adults with LDH/LBP (median age 43, IQR 33–49) and 20 control patients with scoliosis (median age 17, IQR 15–20) underwent surgery at seven Swedish hospitals. Samples were cultured from skin, surgical wound, discs and vertebrae. Genetic relatedness of C. acnes isolates was investigated using single-nucleotide polymorphism analysis. DNA samples collected from discs/vertebrae were analysed using 16S rRNA-based PCR sequencing. MRI findings were assessed for Modic changes.Results: No bacterial growth was found in 6/40 (15%) LDH patients, compared with 3/20 (15%) scoliosis patients. Most positive samples in both groups were isolated from the skin and then from subcutis or deep within the wound. Of the four disc and vertebral samples from each of the 60 patients, 235/240 (98%) were DNA negative by bacterial PCR. A single species, C. acnes, was found exclusively in the disc/vertebra from one patient in each group. In the LDH group, 29/40 (72%) patients had at least one sample with growth of C. acnes, compared to 14/20 (70%) in the scoliosis group. Bacterial findings and Modic changes were not associated.Conclusions: Cutibacterium acnes found in discs and vertebrae during surgery for disc herniation in adults with degenerated discs may be caused by contamination, as findings in this group were similar to findings in a control group of young patients with scoliosis and non-degenerated discs. Furthermore, such findings were almost always combined with bacterial findings on the skin and/or in the wound. There was no association between preoperative Modic changes and bacterial findings. Antibiotic treatment of lumbar disc herniation with sciatica and/or low back pain, without signs of clinical discitis/spondylitis, should be seriously questioned.
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| 2. |
- Abramian, David, 1992-, et al.
(författare)
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Anatomically Informed Bayesian Spatial Priors for FMRI Analysis
- 2020
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Ingår i: ISBI 2020. - : IEEE. - 9781538693308
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Konferensbidrag (refereegranskat)abstract
- Existing Bayesian spatial priors for functional magnetic resonance imaging (fMRI) data correspond to stationary isotropic smoothing filters that may oversmooth at anatomical boundaries. We propose two anatomically informed Bayesian spatial models for fMRI data with local smoothing in each voxel based on a tensor field estimated from a T1-weighted anatomical image. We show that our anatomically informed Bayesian spatial models results in posterior probability maps that follow the anatomical structure.
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| 3. |
- Andersson, Kenneth, 1970-, et al.
(författare)
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A perception based velocity estimator and its use for motion compensated prediction
- 2001
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Ingår i: SCIA 2001 Scandinavian Conference on Image Analysis,2001. ; , s. 493-499
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Konferensbidrag (refereegranskat)abstract
- The use of temporal redundancy is of vital importance for a successful video coding algorithm. An effective approach is the hybrid video coder where motion estimation is used for prediction of the next image frame and code the prediction error, and the motion field. The standard method for motion estimation is block matching as in MPEG-2, typically resulting in block artifacts. In this paper a perception based velocity estimator and its use for pixel based motion compensated prediction of interlaced video is presented.
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| 4. |
- Andersson, Kenneth, 1970-, et al.
(författare)
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Backward-forward motion compensated prediction
- 2002
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Ingår i: Proceedings of ACIVS 2002 (Advanced Concepts for Intelligent Vision Systems), Ghent, Belgium, September 9-11, 2002. ; , s. 260-267
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Konferensbidrag (refereegranskat)abstract
- This paper presents new methods for use of dense motion fields for motion compensation of interlaced video. The motion is estimated using previously decoded field-images. An initial motion compensated prediction is produced using the assumption that the motion is predictable in time. The motion estimation algorithm is phase-based and uses two or three field-images to achieve motion estimates with sub-pixel accuracy. To handle non-constant motion and the specific characteristics of the field-image to be coded, the initially predicted image is refined using forward motion compensation, based on block-matching. Tests show that this approach achieves higher PSNR than forward block-based motion estimation, when coding the residual with the same coder. The subjective performance is also better.
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| 5. |
- Andersson, Kenneth, 1970-, et al.
(författare)
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Continuous normalized convolution
- 2002
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Ingår i: Multimedia and Expo, 2002. ICME '02. Proceedings. 2002 IEEE International Conference on (Volume:1). - : IEEE. - 0780373049 ; , s. 725-728
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Konferensbidrag (refereegranskat)abstract
- The problem of signal estimation for sparsely and irregularly sampled signals is dealt with using continuous normalized convolution. Image values on real-valued positions are estimated using integration of signals and certainties over a neighbourhood employing a local model of both the signal and the used discrete filters. The result of the approach is that an output sample close to signals with high certainty is interpolated using a small neighbourhood. An output sample close to signals with low certainty is spatially predicted from signals in a large neighbourhood.
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| 6. |
- Andersson, Kenneth, 1970-, et al.
(författare)
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Motion compensation using backward prediction and prediction refinement
- 2003
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Ingår i: Signal Processing: Image Communication. - 0923-5965. ; 18:5, s. 381-400
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents new methods for use of dense motion fields for motion compensation of interlaced video. The motion estimation is based on previously decoded field-images. The motion is then temporally predicted and used for motion compensated prediction of the field-image to be coded. The motion estimation algorithm is phase-based and uses two or three field-images to achieve motion estimates with sub-pixel accuracy. To handle non-constant motion and the specific characteristics of the field-image to be coded, the initially predicted image is refined using forward motion compensation, based on block-matching. Tests show that this approach achieves higher PSNR than forward block-based motion estimation, when coding the residual with the same coder. The subjective performance is also better.
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| 7. |
- Andersson, Kenneth, 1970-, et al.
(författare)
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Multiple hierarchical motion estimation
- 2002
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Ingår i: Signal Processing, Pattern Recognition, and Applications - 2002. - : ACTA Press. ; , s. 80-
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Konferensbidrag (refereegranskat)abstract
- This paper introduce multiple hierarchical motion estimation to achieve motion estimates with high spatial resolution. The approach is based on phase-based motion estimation. Results show that the algorithm deal with the smooth motion field of hierarchical motion estimation while keeping the advantages of such an approach.
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| 8. |
- Andersson, Kenneth, 1970-, et al.
(författare)
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Prediction from off-grid samples using continuous normalized convolution
- 2007
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Ingår i: Signal Processing. - : Elsevier BV. - 0165-1684 .- 1872-7557. ; 87:3, s. 353-365
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents a novel method for performing fast estimation of data samples on a desired output grid from samples on an irregularly sampled grid. The output signal is estimated using integration of signals over a neighbourhood employing a local model of the signal using discrete filters. The strength of the method is demonstrated in motion compensation examples by comparing to traditional techniques.
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| 9. |
- Andersson, Mats, 1960-, et al.
(författare)
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Transformation of local spatio-temporal structure tensor fields
- 2003
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Ingår i: Acoustics, Speech, and Signal Processing, 2003. Proceedings. (ICASSP '03). 2003 IEEE International Conference on (Volume:3 ). - : IEEE. - 0780376633 ; , s. 285-288
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Konferensbidrag (refereegranskat)abstract
- Tensors and tensor fields are commonly used in multidimensional signal processing to represent the local structure of the signal. This paper focuses on the case where the sampling on the original signal is anisotropic, e.g when the resolution of the multidimensional image varies depending on the direction which is common e.g. in medical imaging devices. To obtain a geometrically correct description of the local structure there are mainly two possibilities. To resample the image prior to the computation of the local structure tensor field or to compute the tensor field on the original grid and transform the result to obtain a correct geometry of the local structure. This paper deals with the latter alternative and contains an in depth theoretical analysis establishing the appropriate rules for tensor transformations induced by changes in space-time geometry with emphasis on velocity and motion estimation.
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| 10. |
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| 11. |
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| 12. |
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| 13. |
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| 14. |
- Brun, Anders, 1976-, et al.
(författare)
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A tensor-like representation for averaging, filtering and interpolation of 3D object orientation data
- 2005
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Ingår i: Image Processing, 2005. ICIP 2005. IEEE International Conference on (Volume:3 ). - 0780391349 ; , s. 1092-1095
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Konferensbidrag (refereegranskat)abstract
- Averaging, filtering and interpolation of 3-D object orientation data is important in both computer vision and computer graphics, for instance to smooth estimates of object orientation and interpolate between keyframes in computer animation. In this paper we present a novel framework in which the non-linear nature of these problems is avoided by embedding the manifold of 3-D orientations into a 16-dimensional Euclidean space. Linear operations performed in the new representation can be shown to be rotation invariant, and defining a projection back to the orientation manifold results in optimal estimates with respect to the Euclidean metric. In other words, standard linear filters, interpolators and estimators may be applied to orientation data, without the need for an additional machinery to handle the non-linear nature of the problems. This novel representation also provides a way to express uncertainty in 3-D orientation, analogous to the well known tensor representation for lines and hyperplanes.
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| 15. |
- Brun, Anders, 1976-, et al.
(författare)
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Clustering Fiber Traces Using Normalized Cuts
- 2004
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Ingår i: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2004. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783540229766 - 9783540301356 ; , s. 368-375
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Konferensbidrag (refereegranskat)abstract
- In this paper we present a framework for unsupervised segmentation of white matter fiber traces obtained from diffusion weighted MRI data. Fiber traces are compared pairwise to create a weighted undirected graph which is partitioned into coherent sets using the normalized cut (Ncut) criterion. A simple and yet effective method for pairwise comparison of fiber traces is presented which in combination with the Ncut criterion is shown to produce plausible segmentations of both synthetic and real fiber trace data. Segmentations are visualized as colored stream-tubes or transformed to a segmentation of voxel space, revealing structures in a way that looks promising for future explorative studies of diffusion weighted MRI data.
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| 16. |
- Brun, Anders, 1976-, et al.
(författare)
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Coloring of DT-MRI fiber traces using Laplacian Eigenmaps
- 2003
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Ingår i: Computer Aided Systems Theory - EUROCAST 2003. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783540202219 - 9783540452102 ; , s. 518-529
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Konferensbidrag (refereegranskat)abstract
- We propose a novel post processing method for visualization of fiber traces from DT-MRI data. Using a recently proposed non-linear dimensionality reduction technique, Laplacian eigenmaps [3], we create a mapping from a set of fiber traces to a low dimensional Euclidean space. Laplacian eigenmaps constructs this mapping so that similar traces are mapped to similar points, given a custom made pairwise similarity measure for fiber traces. We demonstrate that when the low-dimensional space is the RGB color space, this can be used to visualize fiber traces in a way which enhances the perception of fiber bundles and connectivity in the human brain.
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| 17. |
- Brun, Anders, 1976-, et al.
(författare)
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Fast manifold learning based on Riemannian normal coordinates
- 2005
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Ingår i: Image Analysis. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783540263203 - 9783540315667 ; , s. 920-
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Konferensbidrag (refereegranskat)abstract
- We present a novel method for manifold learning, i.e. identification of the low-dimensional manifold-like structure present in a set of data points in a possibly high-dimensional space. The main idea is derived from the concept of Riemannian normal coordinates. This coordinate system is in a way a generalization of Cartesian coordinates in Euclidean space. We translate this idea to a cloud of data points in order to perform dimension reduction. Our implementation currently uses Dijkstra’s algorithm for shortest paths in graphs and some basic concepts from differential geometry. We expect this approach to open up new possibilities for analysis of e.g. shape in medical imaging and signal processing of manifold-valued signals, where the coordinate system is “learned” from experimental high-dimensional data rather than defined analytically using e.g. models based on Lie-groups.
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| 18. |
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| 19. |
- Brun, Anders, 1976-, et al.
(författare)
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Intrinsic and Extrinsic Means on the Circle -- a Maximum Likelihood Interpretation
- 2007
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Ingår i: ICASSP 2007. IEEE International Conference on Acoustics, Speech and Signal Processing, 2007. - New York, USA : IEEE. - 1424407273 ; , s. III-1053-III-1056
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Konferensbidrag (refereegranskat)abstract
- For data samples in Rn, the mean is a well known estimator. When the data set belongs to an embedded manifold M in Rn, e.g. the unit circle in R2, the definition of a mean can be extended and constrained to M by choosing either the intrinsic Riemannian metric of the manifold or the extrinsic metric of the embedding space. A common view has been that extrinsic means are approximate solutions to the intrinsic mean problem. This paper study both means on the unit circle and reveal how they are related to the ML estimate of independent samples generated from a Brownian distribution. The conclusion is that on the circle, intrinsic and extrinsic means are maximum likelihood estimators in the limits of high SNR and low SNR respectively
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| 20. |
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| 21. |
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| 22. |
- Brun, Anders, 1976-, et al.
(författare)
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Using Importance Sampling for Bayesian Feature Space Filtering
- 2007
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Ingår i: Proceedings of the 15th Scandinavian conference on image analysis. - Berlin, Heidelberg : Springer-Verlag. - 9783540730392 ; , s. 818-827
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Konferensbidrag (refereegranskat)abstract
- We present a one-pass framework for filtering vector-valued images and unordered sets of data points in an N-dimensional feature space. It is based on a local Bayesian framework, previously developed for scalar images, where estimates are computed using expectation values and histograms. In this paper we extended this framework to handle N-dimensional data. To avoid the curse of dimensionality, it uses importance sampling instead of histograms to represent probability density functions. In this novel computational framework we are able to efficiently filter both vector-valued images and data, similar to e.g. the well-known bilateral, median and mean shift filters.
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| 23. |
- Cros, Olivier, et al.
(författare)
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Surface and curve skeleton from a structure tensor analysis applied on mastoid air cells in human temporal bones
- 2017
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Ingår i: IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 2017. - : Institute of Electrical and Electronics Engineers (IEEE). - 9781509011728 - 9781509011735 ; , s. 270-274
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Konferensbidrag (refereegranskat)abstract
- The mastoid of human temporal bone contains numerous air cells connected to each others. In order to gain further knowledge about these air cells, a more compact representation is needed to obtain an estimate of the size distribution of these cells. Already existing skeletonization methods often fail in producing a faithful skeleton mostly due to noise hampering the binary representation of the data. This paper proposes a different approach by extracting geometrical information embedded in the Euclidean distance transform of a volume via a structure tensor analysis based on quadrature filters, from which a secondary structure tensor allows the extraction of surface skeleton along with a curve skeleton from its eigenvalues. Preliminary results obtained on a X-ray micro-CT scans of a human temporal bone show very promising results.
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| 24. |
- Eklund, Anders, 1981-, et al.
(författare)
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Cluster failure revisited: Impact of first level design and physiological noise on cluster false positive rates
- 2019
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 40:7, s. 2017-2032
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 25. |
- Eklund, Anders, 1981-, et al.
(författare)
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Reply to Chen et al.: Parametric methods for cluster inference perform worse for two‐sided t‐tests
- 2019
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 40:5, s. 1689-1691
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- 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.
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