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PUBLICATIONS & PATENTS

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Semantics, Ontologies, Similarity Assessment, Search & Retrieval

Journals:

Semantic Description of Liver CT Images: An Ontological Approach
Kokciyan N., Turkay R., Uskudarli S., Yolum P., Bakır B., Acar B.
IEEE Journal  of Biomedical & Health  Informatics, July 2014, Vol.18/4, pp 1363-1369 pdf / Ask for a preprint

Future PACS for decision support: content-based case retrieval
Akgul C.B. , Acar B.
International Hospital, Vol 38, March/April 2012 pdf / Ask for a preprint

Content Based Image Retrieval in Radiology:Current Status and Future Directions
Akgul C.B., Rubin D.L., Napel S., Beaulieu C.F.,  Greenspan H., Acar B.
Journal of Digital Imaging, 2011, Vol. 24/2, pp 208-222. DOI: 10.1007/s10278-010-9290-9 pdf / Ask for a preprint

Conferences:

General Overview of ImageCLEF at the CLEF 2015 Labs 
Villegas M., Muller H.,  ...,  Acar B, Uskudarli S,  Marvasti NB,  Aldana JF, Garcia M
In Experimental IR Meets Multilinguality, Multimodality and Interaction,
Lecture Notes in Computer Science, Volume 9283, pp. 444-461 URL

ImageCLEF Liver CT Image Annotation Task 2014
Marvasti N.B., Kokciyan N., Turkay R., Yazici A., Yolum P., Uskudarli S., Acar B.
In CLEF 2104 Working Notes, CEUR Workshop Proceedings, vol. 1180, pp. 329-340 URL

Clinical Experience Sharing by Similar Case Retrieval
Marvasti N.B., Akgul C.B., Acar B., Kokciyan N., Uskudarli S., Yolum P., Turkey R., Bakir B.
In Proceedings of 1st ACM MM Workshop on Multimedia Indexing and Information Retrieval for Healthcare (ACM MM'13) pdf

ONLIRA - A Semantic Knowledge Representation of Liver CT Images
Kokciyan N., Turkay R., MD,  Uskudarli S., Yolum P., Acar B., PhD; Bakir B., MD
In Proceedings of RSNA 2013, Chicago, IL, USA (Supplement of Radiology)

CARERA – Karaciğer Vakalarında Klinik Deneyim Paylaşım Platformu
Kokciyan N.,Turkay R., Uskudarli S., Yolum P., Bakir B., Acar B.
In Proceedings of Turkiye Radyoloji Kongresi (TURKRAD) 2013, Antalya, Turkey pdf

Image Processing and Analysis for CT Colonography

Journals:

Polyp Enhancing Level Set Evolution of Colon Wall: Method and Pilot Study
Konukoglu E., Acar B., Paik D.S.,Beaulieu CF,Rosenberg J., Napel S.
IEEE Transactions on Medical Imaging, December 2007, Vol. 26-12, pp.1649-1656. pdf / Ask for a preprint

HDF: Heat Diffusion Fields for Polyp Detection in CT Colonography
Konukoglu E., Acar B.
Signal Processing (Elsevier), October 2007, Vol. 87, Issue: 10, pp. 2407-2416. Online DOI link/pdf/Ask for a preprint

Registration of Central Paths and Colonic Polyps between Supine and Prone Scans in CT Colonography
Li P., Napel S., Acar B., Paik D.S., Jeffrey, Jr. R.B., Beaulieu C.F.
Medical Physics, October 2004, Vol. 31, Issue: 10, pp. 2912-2923 pdf /Ask for a preprint

Surface Normal Overlap: A Computer-Aided Detection Algorithm With Application to Colonic Polyps and Lung Nodules in Helical CT
Paik D.S., Beaulieu C.F., Rubin G.D., Acar B., Jeffrey Jr R.B., Yee J., Dey J., Napel S.
IEEE Transactions on Medical Imaging, June 2004, Vol. 23-6, pp. 661-675 pdf / Ask for a preprint

Edge Displacement Field Based-Classification for Improved Detection of Polyps in CT Colonography
Acar B., Beaulieu C.F., Gokturk S.B., Tomasi C., Paik D.S., Jeffrey, Jr. R,B,, Yee J., Napel S.
IEEE Transactions on Medical Imaging, December 2002, Vol. 21-12, pp. 1461-1467 pdf / Ask for a preprint

A statistical 3D pattern processing method for computer aided detection of polyps in CT colonography
Gokturk S.B., Tomasi C., Acar B., Beaulieu C.F., Paik D.S., Jeffrey R.B., Jr., Yee J., Napel S.
IEEE Transactions on Medical Imaging, December 2001, Vol. 20-12, pp. 1251-1260 pdf  / Ask for a preprint

Conferences:

Assessment of MRF Based Joint Scale Selection and Segmentation for 3D Liver Vessel Segmentation
N.B. Marvasti, B. Acar
Proc. Sinyal Isleme ve Uygulamaları Kurultayı (SIU), Kıbrıs, 2013 pdf

Detecting Tubular Structures Via Direct Vector Field Singularity Characterization
A.D. Cabuk, E. Alpay, E., B. Acar
Proc. 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2010), Buenos Aires, Argentina, IEEE, 2010. pdf

Polyp Enhancement Scheme for Improved Detection of Colonic Polyps in CT Colonography
Konukoglu E., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of RSNA 2005, Chicago, IL, USA (Supplement of Radiology) pdf

Registration of Supine and Prone CT Colonography Data Using Dynamic Time Warping: Method and Evaluation
Balci S.K., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of RSNA 2005, Chicago, IL, USA (Supplement of Radiology) pdf

Registration of Supine and Prone CT Colonography Data: Method and Evaluation
Acar B., Napel S., Paik D.S., Li P., Yee J., Beaulieu C.F., Jeffrey Jr. R.B.
Radiology, November 2001, Vol. 221(P), pp. 332 (87th Annual Meeting of Radiological Society of North America (RSNA 2001), Chicago, USA, 25-30 November 2001). pdf

Medial axis registration of supine and prone CT colonography data
Acar B., Napel S., Paik D.S., Li P., Yee J., Jeffrey Jr. R.B., Beaulieu C.F.
In Proceedings of EMBC 2001, Istanbul, Turkey, 25-28 October 2001. pdf

Polyp Enhancement Scheme for Improved Detection of Colonic Polyps in CT Colonography
Konukoglu E., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of RSNA 2005, Chicago, IL, USA (Supplement of Radiology) pdf

Heat Diffusion Based Detection Of Colonic Polyps In CT Colonography
Konukoglu E., Acar B., Paik D.S., Beaulieu C.F., Napel S.
In Proceedings of EUSIPCO 2005, European Signal Processing Conference, Antalya, Turkey (3rd place in EUSIPCO2005 student paper contest)pdf

Computer Aided Detection Of Polyps In Virtual Colonoscopy Using 3D Heat Diffusion Fields
Konukoglu E., Acar B., Paik D., Beaulieu C.F., Napel S.
In Proceedings of.The 5th Int. Symposium on Virtual Colonoscopy, Boston, MA, USA, 2004 pdf

3D Differential Descriptors for Computer Aided Diagnosis of Colonic Polyps in CTC
Acar B., Beaulieu C.F., Paik D.S., Yee J., Jeffrey, Jr. R.B., Napel S.
Radiology, December 2002, Vol. 225(P), pp. 405 (88th Annual Meeting of Radiological Society of North America (RSNA 2002), Chicago, USA, 1-6 December 2002). pdf

Using Optical Flow Fields For Polyp Detection In Virtual Colonoscopy
Acar B., Napel S., Paik D., Gokturk S.B., Tomasi C., Beaulieu C.F.
In Medical Image Computing and Computer-Assisted Intervention ¬– MICCAI 2001 Utrecht, The Netherlands, 14-17 October 2001, W.J. Niessen and M.A. Viergever ed., LNCS 2208, Springer-Verlag, pp. 637-644. pdf

A Learning Method For Automated Polyp Detection
Gokturk S.B., Tomasi C., Acar B., Paik D., Beaulieu C.F., Napel S.
In Medical Image Computing and Computer-Assisted Intervention ¬– MICCAI 2001 Utrecht, The Netherlands, 14-17 October 2001, W.J. Niessen and M.A. Viergever ed., LNCS 2208, Springer-Verlag, pp. 85-93. pdf

Assessment of an optical flow field-based polyp detector for CT colonography
Acar B., Beaulieu C.F., Paik D.S., Gokturk S.B., Tomasi C., Yee J., Napel S.
In Proceedings of 23rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2001), Istanbul, Turkey, 25-28 October 2001. pdf

Theses:

Liver Segmentation in 3D CT Data
Serkan Cimen
Bogazici University, Electrical and Electronics Engineering, Turkey
September 2011. pdf / Ask for a reprint

PELS: Polyp Enhancing Level-Sets for CT Colonography
Ender Konukoglu
Bogazici University, Dept. of Electrical & Electronics Engineering, Turkey
June 2005 pdf / Ask for a reprint

Patents:

Method for matching and registering medical image data.
Acar B., Beaulieu C.F., Paik D.S., Napel S.A., Jeffrey R.B.Jr.
US Patent Office: US7224827 29/05/2007

Method for detecting and classifying a structure of interest in medical images.
Acar B., Beaulieu C.F., Gokturk S.B., Tomasi C., Paik D.S., Jeffrey R.B.Jr., Napel S.A.
US Patent Office: US7272251 18/09/2007

Three-dimensional pattern recognition method to detect shapes in medical images.
Gokturk S.B., Tomasi C., Acar B., Beaulieu C.F., Napel S.A., Paik D.S.
US Patent Office: US7346209 18/03/2008

Heat diffusion based detection of structures of interest in medical images.
Acar B., Konukoglu E., Beaulieu C.F., Napel S.A., Paik D.S.
US Patent Office: US7729739 10/06/2010


Multi-Dimensional Image Processing & Simulation

Journals:

Magnetic resonance and diffusion tensor imaging analyses indicate heterogeneous strains along human medial gastrocnemius fascicles caused by submaximal plantar-flexion activity
Karakuzu A., Pamuk U., Ozturk C., Acar B.and Yucesoy C.A.
Journal of Biomechanics, May 2017, vol. 57, pp. 69-78 pdf /Ask for a preprint


Combined Magnetic Resonance And Diffusion Tensor Imaging Analyses Provide A Powerful Tool For In Vivo Assessment Of Deformation Along Human Muscle Fibers
Pamuk U., Karakuzu A., Ozturk C., Acar B.and Yucesoy C.A., ,
Journal of the Mechanical Behavior of Biomedical Materials, October 2016, vol. 63, pp. 207-219 pdf /Ask for a preprint

Conferences:

Combined Diffusion Tensor and Magnetic Resonance Imaging for in vivo Assessment of Human Muscle Function
Karakuzu A., Pamuk U., Ozturk C., Acar B., Yucesoy C.A.
In Congress of the European College of Sport Science, 2016

Using Advanced MRI Techniques for Estimating Strain Distributions Along Muscle Fibers During Isometric Plantar-Flexion Activity of Human Medial Gastrocnemius, In Vivo
Karakuzu A.,  Pamuk U., Acar B.,  Ozturk C., Yucesoy C.A.
Int. Society of Biomechanics Congress, ISB 2015, Glasgow, UK

MRI and DTI Analyses Combined Provide A Powerful Tool for Quantifying Deformation Along Human Muscle Fibers In Vivo
Pamuk U., Karakuzu A.,  Acar B.,  Ozturk C., Yucesoy C.A.
Int. Society of Biomechanics Congress, ISB 2015, Glasgow, UK

A Multiray Approach To Phased Array US Simulation From CT Images
M. Tuzer, A. Yazici, B. Acar, M. Boyman
Proc. of Computer Assisted Radiology and Surgery (CARS 2015), Barcelona, Spain, 2015

MRI analyses Indicate Non-uniform Human Muscle Tissue Deformations and Confirm Theoretically Anticipated Sarcomere Length Heterogeneity, In Vivo
U Pamuk, A Karakuzu, P Akyazi, B Acar, C Ozturk, CA Yucesoy
18th National Biomedical Engineering Meeting (BIYOMUT), 2014, Istanbul

Theses:

Ultrasound Simulations Using Computed Tomography Images as Priors
Mert Tuzer
Bogazici University, Department of Physics, Turkey
July 2015. Ask for a reprint

Skeletal Muscle Deformation Analysis Using Diffusion Tensor Magnetic Resonance Imaging
Pinar Akyazi
Bogazici University, Electrical & Electronics Eng. Dept., Turkey
August 2013 pdf / Ask for a reprint

Brain Research: dMRI, fMRI Processing and Analysis

Journals:

SMT: A Reliability Based Interactive DTI Tractography Algorithm
Yoldemir B., Acar B., Firat Z., Kilickesmez O.
IEEE Transactions on Medical Imaging, October 2012, Vol. 31-10, pp. 1929-1940.pdf /Ask for a preprint

Characterizing Non-Gaussian Diffusion by Using Generalized Diffusion Tensors
Liu C., Bammer R., Acar B., Moseley M.E.
Magnetic Resonance in Medicine, May 2004, Vol. 51, pp. 924-937. pdf / Ask for a preprint

Analysis and generalized correction of the effect of spatial gradient field distortions in diffusion-weighted imaging
Bammer R., Markl M., Barnett A., Acar B., Alley M.T., Pelc N.J., Glover G.H., Moseley M.E.
Magnetic Resonance in Medicine, September 2003, Vol. 50-3, pp. 560-569. pdf / Ask for a preprint

In vivo MR Tractography Using Diffusion Imaging
Bammer R., Acar B., Moseley M.E.
European J. of Radiology, 2003, Vol. 45-3, pp.223-234 pdf / Ask for a preprint

Conferences:

bootSMT:Bootstrap Split/Merge Fiber Tractography for DT-MRI Data
Yoldemir A.B., Acar B.
RSNA 2011, Chicago, USA

A Pointwise Correspondence Based DT-MRI Fiber Similarity Measure
Berkiten S., Acar B.
Proc. 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2010), Buenos Aires, Argentina, IEEE, 2010. pdf

SMT: Split & Merge Fiber Tractography for DT-MRI
Bozkaya U., Acar B.
Lecture Notes in Computer Science, Vol. 4792, pp.153-160 ; Springer, 2007 (MICCAI 2007, Brisbane, Australia) pdf

DT-MRI Connectivity And/Or Tractography?: Two New Algorithms
Acar B.
EU FP7 SIMILAR NoE, WP10, Workshop on Tensor Toolboxes, 15-17 November, 2006, Las Palmas, Gran Canaria, Spain. pdf

A Physical Model for MR-DTI Based Connectivity Map Computation
Yoruk E., Acar B., Bammer R.
Lecture Notes in Computer Science, Vol. 3749 / Part  1, pp. 213-220, Springer, 2005 (MICCAI 2005, Palm Springs, CA) pdf

Structure Preserving Regularization Of DT-MRI Vector Fields by Nonlinear Anisotropic Diffusion Filtering
Yoruk E., Acar B.
Proceedings of EUSIPCO 2005, European Signal Processing Conference, Antalya, Turkey pdf

SNR Dependence of DTI Fiber Tracking Protocols
Aksoy M., Acar B., Bammer R.
ISMRM Workshop on Methods for Quantitative Diffusion MRI of Human Brain, 13-16 March 2005, Lake Louise, Alberta, Canada pdf

Comparative Assessment Of DT-MRI Fiber Tractography Algorithms
Acar B., Bammer R., Moseley M.E.
Proceedings of ISMRM 2003, pp. 2164, July 2003, Toronto, Canada pdf

Generalized Diffusion Tensor Imaging (GDTI) Using Higher Order Tensor (HOT) Statistics
Liu C., Bammer R., Acar B., Moseley M.E.
Proceedings of ISMRM 2003, pp. 242,July 2003, Toronto, Canada pdf

Book Chapters/Sections:

DT-MRI Connectivity and/or Tractography?: Two New Algorithms
Acar, B., Yoruk, E.
Tensors in Image Processing and Computer Vision, Aja-Fernández, S.; de Luis García, R.; Tao, D.; Li, X. (Eds.), Series: Advances in Pattern Recognition, ISBN: 978-1-84882-298-6, Springer, 2009 Ask for a reprint

Similar Tensor Arrays: A Framework for Storage of Tensor Array Data
Brun, A., Martin-Fernandez, M., Acar, B., Munoz-Moreno, E., Cammoun, L., Sigfridsson, A., Sosa-Cabrera, D., Svensson, B., Herberthson, M., Knutsson, H.
Tensors in Image Processing and Computer Vision, Aja-Fernández, S.; de Luis García, R.; Tao, D.; Li, X. (Eds.), Series: Advances in Pattern Recognition, ISBN: 978-1-84882-298-6, Springer, 2009 Ask for a reprint

Theses:


Assessing DT-MRI Tractography Results via Sampling The Fiber Tract Space
A. Burak Yoldemir
Bogazici University, Electrical & Electronics Eng. Dept., Turkey
June 2011 pdf / Ask for a reprint

Diffusion Tensor Field Visualization
Sila Girgin
Bogazici University, Computer Engineering, Turkey
January 2008. Ask for a reprint

SMT: Split/Merge Fiber Tractography
Ugur Bozkaya
Bogazici University, Institute of Biomedical Engineering, Turkey
May 2006 pdf / Ask for a reprint

Patents:

Characterization and Correction of Spatial Gradient Field Nonuniformities.
Bammer R., Markl M., Acar B., Pelc N., Moseley M.E.
US Patent Office: US6969991 17/06/2004 (Licensed by GE)


ECG Processing and Analysis

Journals:

QT dispersion does not represent electrocardiographic interlead heterogeneity of ventricular repolarization
Malik, M., Acar, B., Gang, Y., Yap, Y.G., Hnatkova, K., Camm, A.J.
Journal Of Cardiovascular Electrophysiology, 11(8), 835-843 (2000)

Analysis of 12-lead T-wave morphology for risk stratification after myocardial infarction
Zabel, M., Acar, B., Klingenheben, T., Franz, M.R., Hohnloser, S.H., Malik, M.
Circulation, 102(11), 1252-1257 (2000)

Automatic Ectopic Beat Elimination In Short-term Heart Rate Variability Measurement
Acar, B., Savelieva, I., Hemingway H., Malik, M.
Computer Methods And Programs In Biomedicine, 63(2), 123-131 (2000)

SVD Based Online Exercise ECG Signal Orthogonalization
Acar, B., KŲymen, H.
IEEE Transactions On Biomedical Engineering, 46(3), 311-321 (1999)

Spatial, Temporal And Wavefront Direction Characteristics Of 12-Lead T Wave Morphology
Acar, B., Yi, G., Hnatkova K.,  Malik, M.
Medical & Biological Engineering & Computing, 37(5), 574-584 (1999)

New approaches to T-wave analysis from surface ECG
Acar, B.
Cardiac ElectroPhysiology Review (CEPR), 3(4), 319-323 (1999), CEPR has been merged into Journal of Interventional Cardiac Electrophysiology

Patents:

Methods of characterizing ventricular operations and applications thereof
Malik, M., Acar B., Batchvarov V.N.. US Patent Office: US6438409 20/08/2002

Methods of characterizing ventricular operations and applications thereof
Acar B., Batchvarov V.N., Malik, M.,. European Patent Office: EP1038498 27/09/2000


Software Development and Human-Computer Interaction

Journals:

Masterpiece: Physical Interaction and 3D Content-Based Search in VR Applications
Moustakas K., Tzovaras D., Strintzis M. G., Carbini S., Bernier O., Viallet J.E., Raidt S., Mancas M., Dimiccoli M., Yagci E., Balci S., Leon E.I.
IEEE Multimedia Magazine, Vol 13/3, pp. 92-100, June 2006 pdf

Conferences:

DTI Application with Haptic Interfaces
M. Aksoy, N. Avcu, S. Merino-Caviedes, D. Diktas, M.A. Martin-Fernandez, S. Girgin, I. Marras, E. Munoz-Moreno, E. Tekeli, B. Acar, R. Bammer, M. Martin-Fernandez, A.V. Sahiner, S. Uskudarli
Proceedings of Enterface 2007 Workshop, EU 6th Framework Programme SIMILAR NoE, Istanbul, Turkey, July-August 2007 pdf

A Stereo Tracking System For Arbitrary Slicing Of Volumetric Radiological Data
Yagci E., Acar B.
Sinyal Isleme ve Uygulamalari Kurultayi, SIU 2007, Eskisehir, Turkey, June 2007 pdf

VAVframe: A New Concept in Platform Design
Durusut E., Bozkaya U., Yagci E., Acar B.
EUROCON 2005, Serbia & Montenegro, Belgrade, November 22-24, 2005 pdf

Theses:

3D Stylus: A Human Computer Interface For 3D Environment
Enver Yagci
Bogazici University, System & Control Engineering, Turkey
June 2007. pdf /Ask for a reprint

VAVframe: Volumetric Analysis and Visualization Framework
Erhan Durusut
Bogazici University, Dept. of Computer Engineering, Turkey
April 2005. pdf / Ask for a reprint