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- Brusini, Irene, et al.
(author)
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Voxel-Wise Clustering of Tractography Data for Building Atlases of Local Fiber Geometry
- 2019
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Conference paper (peer-reviewed)abstract
- This paper aims at proposing a method to generate atlases of white matter fibers’ geometry that consider local orientation and curvature of fibers extracted from tractography data. Tractography was performed on diffusion magnetic resonance images from a set of healthy subjects and each tract was characterized voxel-wise by its curvature and Frenet–Serret frame, based on which similar tracts could be clustered separately for each voxel and each subject. Finally, the centroids of the clusters identified in all subjects were clustered to create the final atlas. The proposed clustering technique showed promising results in identifying voxel-wise distributions of curvature and orientation. Two tractography algorithms (one deterministic and one probabilistic) were tested for the present work, obtaining two different atlases. A high agreement between the two atlases was found in several brain regions. This suggests that more advanced tractography methods might only be required for some specific regions in the brain. In addition, the probabilistic approach resulted in the identification of a higher number of fiber orientations in various white matter areas, suggesting it to be more adequate for investigating complex fiber configurations in the proposed framework as compared to deterministic tractography.
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| 4. |
- Chowdhury, Manish, et al.
(author)
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Segmentation of Cortical Bone using Fast Level Sets
- 2017
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In: MEDICAL IMAGING 2017. - : SPIE - International Society for Optical Engineering. - 9781510607118
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Conference paper (peer-reviewed)abstract
- Cortical bone plays a big role in the mechanical competence of bone. The analysis of cortical bone requires accurate segmentation methods. Level set methods are usually in the state-of-the-art for segmenting medical images. However, traditional implementations of this method are computationally expensive. This drawback was recently tackled through the so-called coherent propagation extension of the classical algorithm which has decreased computation times dramatically. In this study, we assess the potential of this technique for segmenting cortical bone in interactive time in 3D images acquired through High Resolution peripheral Quantitative Computed Tomography (HR-pQCT). The obtained segmentations are used to estimate cortical thickness and cortical porosity of the investigated images. Cortical thickness and Cortical porosity is computed using sphere fitting and mathematical morphological operations respectively. Qualitative comparison between the segmentations of our proposed algorithm and a previously published approach on six images volumes reveals superior smoothness properties of the level set approach. While the proposed method yields similar results to previous approaches in regions where the boundary between trabecular and cortical bone is well defined, it yields more stable segmentations in challenging regions. This results in more stable estimation of parameters of cortical bone. The proposed technique takes few seconds to compute, which makes it suitable for clinical settings.
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| 5. |
- Jörgens, Daniel, 1988-, et al.
(author)
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Clustering of tensor votes for inference of fibre orientations in DTI data
- 2016
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Conference paper (other academic/artistic)abstract
- mong the various diffusion MRI techniques, diffusion ten-sor imaging (DTI) is still most commonly used in clinicalpractice in order to investigate connectivity and fibre anatomyin the human brain. Besides its apparent advantages of a shortacquisition time and noise robustness compared to other tech-niques, it suffers from its major weakness of assuming a sin-gle fibre model in each voxel. This constitutes a problem forDTI fibre tracking algorithms in regions with crossing fibres.Methods approaching this problem in a postprocessing stepemploy diffusion-like techniques to correct the directional in-formation. We propose an extension of tensor voting in whichinformation from voxels with a single fibre is used to inferorientation distributions in multi fibre voxels. The method isable to resolve multiple fibre orientations by clustering tensorvotes instead of adding them up. Moreover, a new vote cast-ing procedure is proposed which is appropriate even for smallneighbourhoods. To account for the locality of DTI data, weuse a small neighbourhood for distributing information at atime, but apply the algorithm iteratively to close larger gaps.The method shows promising results in both synthetic casesand for processing DTI-data of the human brain.
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| 6. |
- Jörgens, Daniel, 1988-
(author)
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Development and application of rule- and learning-based approaches within the scope of neuroimaging : Tensor voting, tractography and machine learning
- 2020
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Doctoral thesis (other academic/artistic)abstract
- The opportunity to non-invasively probe the structure and function of different parts of the human body makes medical imaging an indispensable tool in clinical diagnostics and related fields of research. Especially neuroscientists rely on modalities like structural or functional Magnetic Resonance Imaging, Computed Tomography or Positron Emission Tomography to study the human brain in vivo. But also in clinical routine, diagnosis, screening or follow-up of different pathological conditions build upon the use of neuroimaging.Computational solutions are essential for the analysis of medical images. While in the case of conventional photography the recorded signal comprises the actual image, most medical imaging devices require the reconstruction of an image from the acquired data. However, not only the image formation, but also further processing tasks to assist doctors or researchers in the interpretation of the data and eventually in subsequent decision making, rely more and more on automation. Typical tasks range from locating and measuring objects in a single patient, e.g. a particular organ, a tumour or a specific region in the brain, to comparing such measurements over time between groups consisting of large numbers of subjects. Automated solutions for these scenarios are required to model complex relations of data in the presence of acquisition noise and subject variability while assuring a tractable computational demand.Traditionally, the development of computational algorithms for medical imaging problems focused on rule-based strategies. Explicitly defined rules that encode the knowledge of the developer are characteristic for such approaches. Within the last decade, this paradigm began to change and learning-based models dramatically gained in popularity. These rely on fitting a complex model to large amounts of data samples, often annotated, which are representative for a particular problem. Instead of manually designing the sought-after solution, it is ‘learned from the data’. While these models have shown enormous potential, they also pose important questions for method developers. How can I get hold of enough data? How much data is enough? How can I obtain proper annotations?This thesis comprises six studies covering the development and the application of methods along the whole pipeline of medical image analysis. Studies I and II propose different extensions to the method of tensor voting to make it applicable in specific medical imaging problems. Studies III–V address the use of modern machine learning techniques, in particular neural networks, in the field of tractography. Notably, the challenge of obtaining adequately annotated data samples is a topic in Study V. In Study VI, a prospective neuroimaging study of unilateral ear canal atresia in adults is presented, covering the application of methods from data acquisition to group comparison. Overall, the compiled works contributed, in one way or the other, to the non-invasive extraction of knowledge from the human body through automated processing of medical images.
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| 7. |
- Jörgens, Daniel, 1988-, et al.
(author)
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Learning a single step of streamline tractography based on neural networks
- 2018
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In: Computational Diffusion MRI. - Cham : Springer Nature. ; , s. 103-116
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Book chapter (other academic/artistic)abstract
- This paper focuses on predicting a single step of streamline tractography from diffusion magnetic resonance imaging data by using different predictors based on neural networks. We train 18 different classifiers in order to assess the effect of including neighbourhood information in the learning step or as a post processing step. Moreover, the performance using four different post processing approaches as well as the variation of the number of classes resulting in a total of 60 experimental configurations are assessed. Further, a comparison to 12 regression-based networks is performed and the effect of including several streamline steps in the network input is investigated. All networks are trained and tested on the ISMRM 2015 tractography challenge data. Our results do not indicate a clear improvement when using neighbouring data (regardless if it used as an input or as a post processing). Also, the linear interpolation of the diffusion data does not outperform the less expensive nearest neighbour approach. As opposed to that, using a linear model on top of the output of the classifiers is beneficial and—in combination with at least 200 classes—resulted in a similar performance as the regression approach. Finally, providing the networks with additional curvature information led to a clear improvement of prediction performance. Our analysis of accuracy based on average angular errors suggests that also considering spatial location in the learning step might further improve machine learning-based streamline tractography algorithms.
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| 8. |
- Jörgens, Daniel, 1988-, et al.
(author)
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Steering second-order tensor voting by vote clustering
- 2016
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Conference paper (peer-reviewed)abstract
- Among the various diffusion MRI techniques, diffusion tensor imaging (DTI) is still most commonly used in clinical practice in order to investigate connectivity and fibre anatomy in the human brain. Besides its apparent advantages of a short acquisition time and noise robustness compared to other techniques, it suffers from its major weakness of assuming a single fibre model in each voxel. This constitutes a problem for DTI fibre tracking algorithms in regions with crossing fibres. Methods approaching this problem in a postprocessing step employ diffusion-like techniques to correct the directional information. We propose an extension of tensor voting in which information from voxels with a single fibre is used to infer orientation distributions in multi fibre voxels. The method is able to resolve multiple fibre orientations by clustering tensor votes instead of adding them up. Moreover, a new vote casting procedure is proposed which is appropriate even for small neighbourhoods. To account for the locality of DTI data, we use a small neighbourhood for distributing information at a time, but apply the algorithm iteratively to close larger gaps. The method shows promising results in both synthetic cases and for processing DTI-data of the human brain.
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