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Endothelial dysfunction assessed by digital tonometry and discrepancy between fraction flow reserve and instantaneous wave free ratio.

Jerabek S, Zemanek D, Pudil J, Bayerova K, Kral A, Kopriva K, Kawase Y, Omori H, Tanigaki T, Chen Z, Vodzinska A, Branny M, Matsuo H, Mates M, Sonka M, Kovarnik T.

Acta Cardiol. 2019 Apr 4:1-6. doi: 10.1080/00015385.2019.1586089. [Epub ahead of print]


Quantitative 3D Analysis of Coronary Wall Morphology in Heart Transplant Patients: OCT-Assessed Cardiac Allograft Vasculopathy Progression.

Chen Z, Pazdernik M, Zhang H, Wahle A, Guo Z, Bedanova H, Kautzner J, Melenovsky V, Kovarnik T, Sonka M.

Med Image Anal. 2018 Dec;50:95-105. doi: 10.1016/ Epub 2018 Sep 14.


Learning-Based Cost Functions for 3-D and 4-D Multi-Surface Multi-Object Segmentation of Knee MRI: Data From the Osteoarthritis Initiative.

Kashyap S, Zhang H, Rao K, Sonka M.

IEEE Trans Med Imaging. 2018 May;37(5):1103-1113. doi: 10.1109/TMI.2017.2781541.


Early detection of cardiac allograft vasculopathy using highly automated 3-dimensional optical coherence tomography analysis.

Pazdernik M, Chen Z, Bedanova H, Kautzner J, Melenovsky V, Karmazin V, Malek I, Tomasek A, Ozabalova E, Krejci J, Franekova J, Wahle A, Zhang H, Kovarnik T, Sonka M.

J Heart Lung Transplant. 2018 Aug;37(8):992-1000. doi: 10.1016/j.healun.2018.04.002. Epub 2018 Apr 6.


Plaque volume and plaque risk profile in diabetic vs. non-diabetic patients undergoing lipid-lowering therapy: a study based on 3D intravascular ultrasound and virtual histology.

Kovarnik T, Chen Z, Mintz GS, Wahle A, Bayerova K, Kral A, Chval M, Kopriva K, Lopez J, Sonka M, Linhart A.

Cardiovasc Diabetol. 2017 Dec 7;16(1):156. doi: 10.1186/s12933-017-0637-0.


Development of a radiobiological evaluation tool to assess the expected clinical impacts of contouring accuracy between manual and semi-automated segmentation algorithms.

Yusung Kim, Patwardhan KA, Beichel RR, Smith BJ, Mart C, Plichta KA, Chang T, Sonka M, Graham MM, Magnotta V, Casavant T, Junyi Xia, Buatti JM.

Conf Proc IEEE Eng Med Biol Soc. 2017 Jul;2017:3409-3412. doi: 10.1109/EMBC.2017.8037588.


CorteXpert: A model-based method for automatic renal cortex segmentation.

Xiang D, Bagci U, Jin C, Shi F, Zhu W, Yao J, Sonka M, Chen X.

Med Image Anal. 2017 Dec;42:257-273. doi: 10.1016/ Epub 2017 Aug 23.


Spatial Correspondence Between Intraretinal Fluid, Subretinal Fluid, and Pigment Epithelial Detachment in Neovascular Age-Related Macular Degeneration.

Klimscha S, Waldstein SM, Schlegl T, Bogunovic H, Sadeghipour A, Philip AM, Podkowinski D, Pablik E, Zhang L, Abramoff MD, Sonka M, Gerendas BS, Schmidt-Erfurth U.

Invest Ophthalmol Vis Sci. 2017 Aug 1;58(10):4039-4048. doi: 10.1167/iovs.16-20201.


Optical Coherence Tomography Analysis Based Prediction of Humphrey 24-2 Visual Field Thresholds in Patients With Glaucoma.

Guo Z, Kwon YH, Lee K, Wang K, Wahle A, Alward WLM, Fingert JH, Bettis DI, Johnson CA, Garvin MK, Sonka M, Abràmoff MD.

Invest Ophthalmol Vis Sci. 2017 Aug 1;58(10):3975-3985. doi: 10.1167/iovs.17-21832.


Predicting Locations of High-Risk Plaques in Coronary Arteries in Patients Receiving Statin Therapy.

Zhang L, Wahle A, Chen Z, Lopez JJ, Kovarnik T, Sonka M.

IEEE Trans Med Imaging. 2018 Jan;37(1):151-161. doi: 10.1109/TMI.2017.2725443. Epub 2017 Jul 11.


Globally Optimal Label Fusion with Shape Priors.

Oguz I, Kashyap S, Wang H, Yushkevich P, Sonka M.

Med Image Comput Comput Assist Interv. 2016 Oct;9901:538-546. doi: 10.1007/978-3-319-46723-8_62. Epub 2016 Oct 2.


Automated Segmentation of Knee MRI Using Hierarchical Classifiers and Just Enough Interaction Based Learning: Data from Osteoarthritis Initiative.

Kashyap S, Oguz I, Zhang H, Sonka M.

Med Image Comput Comput Assist Interv. 2016 Oct;9901:344-351. doi: 10.1007/978-3-319-46723-8_40. Epub 2016 Oct 2.


Machine learning in a graph framework for subcortical segmentation.

Guo Z, Kashyap S, Sonka M, Oguz I.

Proc SPIE Int Soc Opt Eng. 2017 Feb 11;10133. pii: 101330H. doi: 10.1117/12.2254874. Epub 2017 Feb 24.


A machine-learning graph-based approach for 3D segmentation of Bruch's membrane opening from glaucomatous SD-OCT volumes.

Miri MS, Abràmoff MD, Kwon YH, Sonka M, Garvin MK.

Med Image Anal. 2017 Jul;39:206-217. doi: 10.1016/ Epub 2017 May 6.


Graph-based segmentation of abnormal nuclei in cervical cytology.

Zhang L, Kong H, Liu S, Wang T, Chen S, Sonka M.

Comput Med Imaging Graph. 2017 Mar;56:38-48. doi: 10.1016/j.compmedimag.2017.01.002. Epub 2017 Jan 31.


Cystatin C Is Associated with the Extent and Characteristics of Coronary Atherosclerosis in Patients with Preserved Renal Function.

Král A, Kovárník T, Vaníčková Z, Skalická H, Horák J, Bayerová K, Chen Z, Wahle A, Zhang L, Kopřiva K, Benáková H, Sonka M, Linhart A.

Folia Biol (Praha). 2016;62(6):225-234.


Nerve Fiber Layer Thickness and Characteristics Associated with Glaucoma in Community Living Older Adults: Prelude to a Screening Trial?

Klein BE, Johnson CA, Meuer SM, Lee K, Wahle A, Lee KE, Kulkarni A, Sonka M, Abràmoff MD, Klein R.

Ophthalmic Epidemiol. 2017 Apr;24(2):104-110. doi: 10.1080/09286586.2016.1258082. Epub 2016 Dec 29.


4D Graph-Based Segmentation for Reproducible and Sensitive Choroid Quantification From Longitudinal OCT Scans.

Oguz I, Abramoff MD, Zhang L, Lee K, Zhang EZ, Sonka M.

Invest Ophthalmol Vis Sci. 2016 Jul 1;57(9):OCT621-OCT630. doi: 10.1167/iovs.15-18924.


Pathologic Intimal Thickening Plaque Phenotype: Not as Innocent as Previously Thought. A Serial 3D Intravascular Ultrasound Virtual Histology Study.

Kovarnik T, Chen Z, Wahle A, Zhang L, Skalicka H, Kral A, Lopez JJ, Horak J, Sonka M, Linhart A.

Rev Esp Cardiol (Engl Ed). 2017 Jan;70(1):25-33. doi: 10.1016/j.rec.2016.04.058. Epub 2016 Sep 5. English, Spanish.


Quantitative analysis of retinal OCT.

Sonka M, Abràmoff MD.

Med Image Anal. 2016 Oct;33:165-169. doi: 10.1016/ Epub 2016 Jul 12.


Evaluation of Variable Thin-Cap Fibroatheroma Definitions and Association of Virtual Histology-Intravascular Ultrasound Findings With Cavity Rupture Size.

Hirai T, Chen Z, Zhang L, Baaj S, Kovarnik T, Porcaro K, Kaminski J, Hawn S, Agrawal A, Makki N, Downe R, Wahle A, Sonka M, Lopez JJ.

Am J Cardiol. 2016 Jul 15;118(2):162-9. doi: 10.1016/j.amjcard.2016.04.050. Epub 2016 May 4.


Semiautomated segmentation of head and neck cancers in 18F-FDG PET scans: A just-enough-interaction approach.

Beichel RR, Van Tol M, Ulrich EJ, Bauer C, Chang T, Plichta KA, Smith BJ, Sunderland JJ, Graham MM, Sonka M, Buatti JM.

Med Phys. 2016 Jun;43(6):2948-2964. doi: 10.1118/1.4948679.


Non-invasive endothelial function assessment using digital reactive hyperaemia correlates with three-dimensional intravascular ultrasound and virtual histology-derived plaque volume and plaque phenotype.

Kovarnik T, Jerabek S, Chen Z, Wahle A, Zhang L, Dostalova G, Skalicka H, Kral A, Horak J, Sonka M, Linhart A.

Kardiol Pol. 2016;74(12):1485-1491. doi: 10.5603/KP.a2016.0062. Epub 2016 May 10.


Retinal neurodegeneration may precede microvascular changes characteristic of diabetic retinopathy in diabetes mellitus.

Sohn EH, van Dijk HW, Jiao C, Kok PH, Jeong W, Demirkaya N, Garmager A, Wit F, Kucukevcilioglu M, van Velthoven ME, DeVries JH, Mullins RF, Kuehn MH, Schlingemann RO, Sonka M, Verbraak FD, Abràmoff MD.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):E2655-64. doi: 10.1073/pnas.1522014113. Epub 2016 Apr 25.


Automated Segmentability Index for Layer Segmentation of Macular SD-OCT Images.

Lee K, Buitendijk GH, Bogunovic H, Springelkamp H, Hofman A, Wahle A, Sonka M, Vingerling JR, Klaver CC, Abràmoff MD.

Transl Vis Sci Technol. 2016 Apr 5;5(2):14. eCollection 2016 Mar.


Evaluating Efficacy of Aflibercept in Refractory Exudative Age-Related Macular Degeneration With OCT Segmentation Volumetric Analysis.

Choi CS, Zhang L, Abràmoff MD, Sonka M, Shifera AS, Kay CN.

Ophthalmic Surg Lasers Imaging Retina. 2016 Mar;47(3):245-51. doi: 10.3928/23258160-20160229-07.


Choroidal thickness maps from spectral domain and swept source optical coherence tomography: algorithmic versus ground truth annotation.

Philip AM, Gerendas BS, Zhang L, Faatz H, Podkowinski D, Bogunovic H, Abramoff MD, Hagmann M, Leitner R, Simader C, Sonka M, Waldstein SM, Schmidt-Erfurth U.

Br J Ophthalmol. 2016 Oct;100(10):1372-6. doi: 10.1136/bjophthalmol-2015-307985. Epub 2016 Jan 14.


Simultaneous Registration of Location and Orientation in Intravascular Ultrasound Pullbacks Pairs Via 3D Graph-Based Optimization.

Zhang L, Wahle A, Chen Z, Zhang L, Downe RW, Kovarnik T, Sonka M.

IEEE Trans Med Imaging. 2015 Dec;34(12):2550-61. doi: 10.1109/TMI.2015.2444815. Epub 2015 Jun 11.


LOGISMOS-B for Primates: Primate Cortical Surface Reconstruction and Thickness Measurement.

Oguz I, Styner M, Sanchez M, Shi Y, Sonka M.

Proc SPIE Int Soc Opt Eng. 2015;9413. pii: 941313.


Validity of Automated Choroidal Segmentation in SS-OCT and SD-OCT.

Zhang L, Buitendijk GH, Lee K, Sonka M, Springelkamp H, Hofman A, Vingerling JR, Mullins RF, Klaver CC, Abràmoff MD.

Invest Ophthalmol Vis Sci. 2015 May;56(5):3202-11. doi: 10.1167/iovs.14-15669.


Thickness mapping of eleven retinal layers segmented using the diffusion maps method in normal eyes.

Kafieh R, Rabbani H, Hajizadeh F, Abramoff MD, Sonka M.

J Ophthalmol. 2015;2015:259123. doi: 10.1155/2015/259123. Epub 2015 Apr 19.


Quantitative analysis of retinal layers' optical intensities on 3D optical coherence tomography for central retinal artery occlusion.

Chen H, Chen X, Qiu Z, Xiang D, Chen W, Shi F, Zheng J, Zhu W, Sonka M.

Sci Rep. 2015 Mar 18;5:9269. doi: 10.1038/srep09269.


Stratified Sampling Voxel Classification for Segmentation of Intraretinal and Subretinal Fluid in Longitudinal Clinical OCT Data.

Xiayu Xu, Kyungmoo Lee, Li Zhang, Sonka M, Abramoff MD.

IEEE Trans Med Imaging. 2015 Jul;34(7):1616-1623. doi: 10.1109/TMI.2015.2408632. Epub 2015 Mar 6.


Comparison of retinal and choriocapillaris thicknesses following sitting to supine transition in healthy individuals and patients with age-related macular degeneration.

Almeida DR, Zhang L, Chin EK, Mullins RF, Kucukevcilioglu M, Critser DB, Sonka M, Stone EM, Folk JC, Abràmoff MD, Russell SR.

JAMA Ophthalmol. 2015 Mar;133(3):297-303. doi: 10.1001/jamaophthalmol.2014.5168.


Relationships of retinal structure and humphrey 24-2 visual field thresholds in patients with glaucoma.

Bogunović H, Kwon YH, Rashid A, Lee K, Critser DB, Garvin MK, Sonka M, Abràmoff MD.

Invest Ophthalmol Vis Sci. 2014 Dec 9;56(1):259-71. doi: 10.1167/iovs.14-15885.


Robust cortical thickness measurement with LOGISMOS-B.

Oguz I, Sonka M.

Med Image Comput Comput Assist Interv. 2014;17(Pt 1):722-30.


Automated 3-D retinal layer segmentation of macular optical coherence tomography images with serous pigment epithelial detachments.

Shi F, Chen X, Zhao H, Zhu W, Xiang D, Gao E, Sonka M, Chen H.

IEEE Trans Med Imaging. 2015 Feb;34(2):441-52. doi: 10.1109/TMI.2014.2359980. Epub 2014 Sep 24.


Three-dimensional automated choroidal volume assessment on standard spectral-domain optical coherence tomography and correlation with the level of diabetic macular edema.

Gerendas BS, Waldstein SM, Simader C, Deak G, Hajnajeeb B, Zhang L, Bogunovic H, Abramoff MD, Kundi M, Sonka M, Schmidt-Erfurth U.

Am J Ophthalmol. 2014 Nov;158(5):1039-48. doi: 10.1016/j.ajo.2014.08.001. Epub 2014 Aug 12.


Multi-surface and multi-field co-segmentation of 3-D retinal optical coherence tomography.

Bogunovic H, Sonka M, Kwon YH, Kemp P, Abramoff MD, Wu X.

IEEE Trans Med Imaging. 2014 Dec;33(12):2242-53. doi: 10.1109/TMI.2014.2336246. Epub 2014 Jul 9.


LOGISMOS-B: layered optimal graph image segmentation of multiple objects and surfaces for the brain.

Oguz I, Sonka M.

IEEE Trans Med Imaging. 2014 Jun;33(6):1220-35. doi: 10.1109/TMI.2014.2304499. Epub 2014 Feb 7.


Quantifying disrupted outer retinal-subretinal layer in SD-OCT images in choroidal neovascularization.

Zhang L, Sonka M, Folk JC, Russell SR, Abràmoff MD.

Invest Ophthalmol Vis Sci. 2014 Apr 11;55(4):2329-35. doi: 10.1167/iovs.13-13048.


Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain.

Rabbani H, Sonka M, Abramoff MD.

Int J Biomed Imaging. 2013;2013:417491. doi: 10.1155/2013/417491. Epub 2013 Oct 10.


RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI.

Oguz I, Zhang H, Rumple A, Sonka M.

J Neurosci Methods. 2014 Jan 15;221:175-82. doi: 10.1016/j.jneumeth.2013.09.021. Epub 2013 Oct 18.


Reproducibility of SD-OCT-based ganglion cell-layer thickness in glaucoma using two different segmentation algorithms.

Garvin MK, Lee K, Burns TL, Abràmoff MD, Sonka M, Kwon YH.

Invest Ophthalmol Vis Sci. 2013 Oct 25;54(10):6998-7004. doi: 10.1167/iovs.13-12131.


Quantitative analysis of retinal layer optical intensities on three-dimensional optical coherence tomography.

Chen X, Hou P, Jin C, Zhu W, Luo X, Shi F, Sonka M, Chen H.

Invest Ophthalmol Vis Sci. 2013 Oct 21;54(10):6846-51. doi: 10.1167/iovs.13-12062.


Intra-retinal layer segmentation of 3D optical coherence tomography using coarse grained diffusion map.

Kafieh R, Rabbani H, Abramoff MD, Sonka M.

Med Image Anal. 2013 Dec;17(8):907-28. doi: 10.1016/ Epub 2013 Jun 11.


Prediction of coronary vessel involvement on the basis of atherosclerosis risk factor analysis.

Kovarnik T, Kral A, Skalicka H, Skalicka L, Dostal O, Kralik L, Martasek P, Aschermann M, Horak J, Linhart A, Wahle A, Sonka M.

Bratisl Lek Listy. 2013;114(7):413-7. Review.


Adjustment of the retinal angle in SD-OCT of glaucomatous eyes provides better intervisit reproducibility of peripapillary RNFL thickness.

Lee K, Sonka M, Kwon YH, Garvin MK, Abràmoff MD.

Invest Ophthalmol Vis Sci. 2013 Jul 18;54(7):4808-12. doi: 10.1167/iovs.13-12211.


Effect of age on individual retinal layer thickness in normal eyes as measured with spectral-domain optical coherence tomography.

Demirkaya N, van Dijk HW, van Schuppen SM, Abràmoff MD, Garvin MK, Sonka M, Schlingemann RO, Verbraak FD.

Invest Ophthalmol Vis Sci. 2013 Jul 22;54(7):4934-40. doi: 10.1167/iovs.13-11913.


Reproducibility of diabetic macular edema estimates from SD-OCT is affected by the choice of image analysis algorithm.

Sohn EH, Chen JJ, Lee K, Niemeijer M, Sonka M, Abràmoff MD.

Invest Ophthalmol Vis Sci. 2013 Jun 19;54(6):4184-8. doi: 10.1167/iovs.12-10420.

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