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2. Modality agnostic intracranial aneurysm detection through supervised vascular surface classification

Author

Bizjak, Žiga, Likar, Boštjan, Pernuš, Franjo, and Špiclin, Žiga

Subjects
Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Intracranial aneurysms (IAs) are generally asymptomatic and thus often discovered incidentally on angiographic scans like 3D DSA, CTA and MRA. Skilled radiologists achieved a sensitivity of 88% by means of visual detection, which seems inadequate considering that prevalence of IAs in general population is 3-5%. Deep learning models trained and executed on angiographic scans seem best-suited for IA detection, however, reported performances across different modalities is currently insufficient for clinical application. This paper presents a novel modality agnostic method for detection of IAs. First the triangulated surfaces of vascular structures were roughly extracted from the angiograms. For IA detection purpose, the extracted surfaces were randomly parcellated into local patches and then a translation, rotation and scale invariant classifier based on deep neural network (DNN) was trained. Test stage proceeded by mimicking the surface extraction and parcellation at several random locations, then the trained DNN model was applied for classification, and the results aggregated into IA detection heatmaps across entire vascular surface. For training and validation the extracted contours were presented to skilled neurosurgeon, who marked the locations of IAs. The DNN was trained and tested using three-fold cross-validation based on 57 DSAs, 5 CTAs and 5 MRAs and showed a 98.6% sensitivity at 0.2 false positive detections per image. Experimental results show that proposed approach not only significantly improved detection sensitivity and specificity compared to state-of-the-art intensity based methods, but is also modality agnostic and thus better suited for clinical application., Comment: 10 pages, 5 figures

Published
2020

3. Vascular surface segmentation for intracranial aneurysm isolation and quantification

Author

Bizjak, Žiga, Likar, Boštjan, Pernuš, Franjo, and Špiclin, Žiga

Subjects
Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Predicting rupture risk and deciding on optimal treatment plan for intracranial aneurysms (IAs) is possible by quantification of their size and shape. For this purpose the IA has to be isolated from 3D angiogram. State-of-the-art methods perform IA isolation by encoding neurosurgeon's intuition about former non-dilated vessel anatomy through principled approaches like fitting a cutting plane to vasculature surface, using Gaussian curvature and vessel centerline distance constraints, by deformable contours or graph cuts guided by the curvature or restricted by Voronoi surface decomposition and similar. However, the large variability of IAs and their parent vasculature configurations often leads to failure or non-intuitive isolation. Manual corrections are thus required, but suffer from poor reproducibility. In this paper, we aim to increase the accuracy, robustness and reproducibility of IA isolation through two stage deep learning based segmentation of vascular surface. The surface was represented by local patches in form of point clouds, which were fed into first stage multilayer neural network (MNN) to obtain descriptors invariant to point ordering, rotation and scale. Binary classifier as second stage MNN was used to isolate surface belonging to the IA. Method validation was based on 57 DSA, 28 CTA and 5 MRA images, where cross-validation showed high segmentation sensitivity of 0.985, a substantial improvement over 0.830 obtained for the state-of-the-art method on the same datasets. Visual analysis of IA isolation and its high accuracy and reliability consistent across CTA and DSA scans confirmed the clinical applicability of proposed method., Comment: 10 pages, 4 figures, MICCAI conference

Published
2020

5. Segmentation of Pathological Spines in CT Images Using a Two-Way CNN and a Collision-Based Model

Author

Korez, Robert, Likar, Boštjan, Pernuš, Franjo, Vrtovec, Tomaž, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Glocker, Ben, editor, Yao, Jianhua, editor, Vrtovec, Tomaž, editor, Frangi, Alejandro, editor, and Zheng, Guoyan, editor

Published
2018
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6. Predicting Nucleus Basalis of Meynert Volume from Compartmental Brain Segmentations

Author

Madan, Hennadii, Berlot, Rok, Ray, Nicola J., Pernuš, Franjo, Špiclin, Žiga, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Rekik, Islem, editor, Unal, Gozde, editor, Adeli, Ehsan, editor, and Park, Sang Hyun, editor

Published
2018
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9. Benchmarking Quantitative Imaging Biomarker Measurement Methods Without a Gold Standard

Author

Madan, Hennadii, Pernuš, Franjo, Špiclin, Žiga, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Descoteaux, Maxime, editor, Maier-Hein, Lena, editor, Franz, Alfred, editor, Jannin, Pierre, editor, Collins, D. Louis, editor, and Duchesne, Simon, editor

Published
2017
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11. Deformable Model-Based Segmentation of Intervertebral Discs from MR Spine Images by Using the SSC Descriptor

Author

Korez, Robert, Ibragimov, Bulat, Likar, Boštjan, Pernuš, Franjo, Vrtovec, Tomaž, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Vrtovec, Tomaž, editor, Yao, Jianhua, editor, Glocker, Ben, editor, Klinder, Tobias, editor, Frangi, Alejandro, editor, Zheng, Guoyan, editor, and Li, Shuo, editor

Published
2016
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12. Automated Pedicle Screw Size and Trajectory Planning by Maximization of Fastening Strength

Author

Knez, Dejan, Likar, Boštjan, Pernuš, Franjo, Vrtovec, Tomaž, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Vrtovec, Tomaž, editor, Yao, Jianhua, editor, Glocker, Ben, editor, Klinder, Tobias, editor, Frangi, Alejandro, editor, Zheng, Guoyan, editor, and Li, Shuo, editor

Published
2016
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13. Combining Unsupervised and Supervised Methods for Lesion Segmentation

Author

Jerman, Tim, Galimzianova, Alfiia, Pernuš, Franjo, Likar, Boštjan, Špiclin, Žiga, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Crimi, Alessandro, editor, Menze, Bjoern, editor, Maier, Oskar, editor, Reyes, Mauricio, editor, and Handels, Heinz, editor

Published
2016
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14. Manual and Computer-Assisted Pedicle Screw Placement Plans: A Quantitative Comparison

Author

Knez, Dejan, Mohar, Janez, Cirman, Robert J., Likar, Boštjan, Pernuš, Franjo, Vrtovec, Tomaž, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Yao, Jianhua, editor, Vrtovec, Tomaž, editor, Zheng, Guoyan, editor, Frangi, Alejandro, editor, Glocker, Ben, editor, and Li, Shuo, editor

Published
2016
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15. Model-Based Segmentation of Vertebral Bodies from MR Images with 3D CNNs

Author

Korez, Robert, Likar, Boštjan, Pernuš, Franjo, Vrtovec, Tomaž, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Ourselin, Sebastien, editor, Joskowicz, Leo, editor, Sabuncu, Mert R., editor, Unal, Gozde, editor, and Wells, William, editor

Published
2016
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19. Computer-Aided Detection and Quantification of Intracranial Aneurysms

Author

Jerman, Tim, Pernuš, Franjo, Likar, Boštjan, Špiclin, Žiga, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Navab, Nassir, editor, Hornegger, Joachim, editor, Wells, William M., editor, and Frangi, Alejandro, editor

Published
2015
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24. Fast and Robust 3D to 2D Image Registration by Backprojection of Gradient Covariances

Author

Špiclin, Žiga, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Kobsa, Alfred, editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Weikum, Gerhard, editor, Ourselin, Sébastien, editor, and Modat, Marc, editor

Published
2014
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25. Automatic Detection of Misalignment in Rigid 3D-2D Registration

Author

Mitrović, Uroš, Špiclin, Žiga, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Erdt, Marius, editor, Linguraru, Marius George, editor, Oyarzun Laura, Cristina, editor, Shekhar, Raj, editor, Wesarg, Stefan, editor, González Ballester, Miguel Angel, editor, and Drechsler, Klaus, editor

Published
2014
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26. Robust Mixture-Parameter Estimation for Unsupervised Segmentation of Brain MR Images

Author

Galimzianova, Alfiia, Špiclin, Žiga, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Menze, Bjoern, editor, Langs, Georg, editor, Montillo, Albert, editor, Kelm, Michael, editor, Müller, Henning, editor, and Tu, Zhuowen, editor

Published
2014
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28. Robust 3-D/2-D registration of CT and MR to X-ray images based on gradient reconstruction

Author

Markelj, Primož, Tomaževič, Dejan, Pernuš, Franjo, and Likar, Boštjan

Abstract

Abstract: Objective: A novel 3-D/2-D registration method based on matching 3-D pre-interventional image gradients and coarsely reconstructed 3-D gradients from intra-interventional 2-D images is presented. Material and methods: The novel method establishes correspondences between two sets of gradients by searching for correspondences along normals to anatomical structures in 3-D images, while the final correspondences are established in an iterative process, combining the robust random sample consensus algorithm (RANSAC) and a special gradient matching criterion function. The proposed method was evaluated by the publicly available standardized evaluation methodology for 3-D/2-D registration, consisting of 3-D rotational X-ray, computed tomography (CT), magnetic resonance (MR), and 2-D X-ray images of two spine segments, and evaluation criteria. Results: Preliminary results show significant improve- ment in robustness (capture range and success rate) over three well established intensity-based, gradient-based, and reconstruction-based methods. Conclusion: The 3-D/2-D gradient reconstruction-based registration method efficiently combines the advantages of gradient and reconstruction-based methods, thereby enabling robust registration of CT and MR to only two X-ray images, while keeping the computational demands low.

Published
2024
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36. Method for 3D-2D Registration of Vascular Images: Application to 3D Contrast Agent Flow Visualization

Author

Mitrović, Uroš, Špiclin, Žiga, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Drechsler, Klaus, editor, Erdt, Marius, editor, Linguraru, Marius George, editor, Oyarzun Laura, Cristina, editor, Sharma, Karun, editor, Shekhar, Raj, editor, and Wesarg, Stefan, editor

Published
2013
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37. Quad-tree Based Entropy Estimator for Fast and Robust Brain Image Registration

Author

Špiclin, Žiga, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Dawant, Benoît M., editor, Christensen, Gary E., editor, Fitzpatrick, J. Michael, editor, and Rueckert, Daniel, editor

Published
2012
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38. Information-Theoretic Multi-modal Image Registration Based on the Improved Fast Gauss Transform: Application to Brain Images

Author

Špiclin, Žiga, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Liu, Tianming, editor, Shen, Dinggang, editor, Ibanez, Luis, editor, and Tao, Xiaodong, editor

Published
2011
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41. Segmentation of Vertebral Bodies in MR Images Based on Geometrical Models in 3D

Author

Štern, Darko, Likar, Boštjan, Pernuš, Franjo, Vrtovec, Tomaž, Hutchison, David, Kanade, Takeo, Kittler, Josef, Kleinberg, Jon M., Mattern, Friedemann, Mitchell, John C., Naor, Moni, Nierstrasz, Oscar, Pandu Rangan, C., Steffen, Bernhard, Sudan, Madhu, Terzopoulos, Demetri, Tygar, Doug, Vardi, Moshe Y., Weikum, Gerhard, Liao, Hongen, editor, Edwards, P. J. 'Eddie", editor, Pan, Xiaochuan, editor, Fan, Yong, editor, and Yang, Guang-Zhong, editor

Published
2010
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42. A New Image Database for 3D/2D Registration Based on the Visible Human Data Set

Author

Markelj, Primož, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Fischer, Bernd, editor, Dawant, Benoît M., editor, and Lorenz, Cristian, editor

Published
2010
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44. A Symmetry-Based Method for the Determination of Vertebral Rotation in 3D

Author

Vrtovec, Tomaž, Pernuš, Franjo, Likar, Boštjan, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Metaxas, Dimitris, editor, Axel, Leon, editor, Fichtinger, Gabor, editor, and Székely, Gábor, editor

Published
2008
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45. EEG to MRI Registration Based on Global and Local Similarities of MRI Intensity Distributions

Author

Špiclin, Žiga, Hans, Arne, Duffy, Frank H., Warfield, Simon K., Likar, Boštjan, Pernuš, Franjo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Metaxas, Dimitris, editor, Axel, Leon, editor, Fichtinger, Gabor, editor, and Székely, Gábor, editor

Published
2008
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46. 3D/2D Image Registration: The Impact of X-Ray Views and Their Number

Author

Tomaževič, Dejan, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Ayache, Nicholas, editor, Ourselin, Sébastien, editor, and Maeder, Anthony, editor

Published
2007
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47. Generation of Curved Planar Reformations from Magnetic Resonance Images of the Spine

Author

Vrtovec, Tomaž, Ourselin, Sébastien, Gomes, Lavier, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Larsen, Rasmus, editor, Nielsen, Mads, editor, and Sporring, Jon, editor

Published
2006
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48. Evaluation of Similarity Measures for Non-rigid Registration

Author

Škerl, Darko, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Pluim, Josien P. W., editor, Likar, Boštjan, editor, and Gerritsen, Frans A., editor

Published
2006
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50. Reconstruction-Based 3D/2D Image Registration

Author

Tomaževič, Dejan, Likar, Boštjan, Pernuš, Franjo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Duncan, James S., editor, and Gerig, Guido, editor

Published
2005
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