Ipek Oguz

Ipek Oguz

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Ipek Oguz

Publications by authors named "Ipek Oguz"

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45Publications

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Minimally interactive placenta segmentation from three-dimensional ultrasound images.

J Med Imaging (Bellingham) 2020 Jan 22;7(1):014004. Epub 2020 Feb 22.

University of Pennsylvania, Department of Obstetrics and Gynecology, Maternal and Child Health Research Program, Philadelphia, Pennsylvania, United States.

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http://dx.doi.org/10.1117/1.JMI.7.1.014004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035878PMC
January 2020

Joint Intensity Fusion Image Synthesis Applied to Multiple Sclerosis Lesion Segmentation.

Brainlesion 2018 17;10670:43-54. Epub 2018 Feb 17.

Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920684PMC
February 2018

Dice Overlap Measures for Objects of Unknown Number: Application to Lesion Segmentation.

Brainlesion 2018 17;10670:3-14. Epub 2018 Feb 17.

Department of Electrical and Computer Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.

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http://dx.doi.org/10.1007/978-3-319-75238-9_1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920690PMC
February 2018

Multiple Sclerosis Lesion Segmentation Using Joint Label Fusion.

Patch Based Tech Med Imaging (2017) 2017 Sep 31;10530:138-145. Epub 2017 Aug 31.

Penn Image Computing and Science Lab, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1007/978-3-319-67434-6_16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5918408PMC
September 2017

Automated segmentation of the choroid in EDI-OCT images with retinal pathology using convolution neural networks.

Fetal Infant Ophthalmic Med Image Anal (2017) 2017 Sep 9;10554:177-184. Epub 2017 Sep 9.

Department of Radiology, University of Pennsylvania, Philadelphia PA 19104, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947958PMC
http://dx.doi.org/10.1007/978-3-319-67561-9_20DOI Listing
September 2017

Gradient Boosted Trees for Corrective Learning.

Mach Learn Med Imaging 2017 Sep 7;10541:203-211. Epub 2017 Sep 7.

University Pennsylvania, Philadelphia, PA 19104, USA.

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http://link.springer.com/10.1007/978-3-319-67389-9_24
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http://dx.doi.org/10.1007/978-3-319-67389-9_24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186453PMC
September 2017

Machine learning in a graph framework for subcortical segmentation.

Proc SPIE Int Soc Opt Eng 2017 Feb 24;10133. Epub 2017 Feb 24.

Dept. of Radiology, University of Pennsylvania, Philadelphia, PA, USA 19104.

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http://dx.doi.org/10.1117/12.2254874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471906PMC
February 2017

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

Med Image Comput Comput Assist Interv 2016 Oct 2;9901:344-351. Epub 2016 Oct 2.

Iowa Institute for Biomedical Imaging, The University of Iowa, Iowa City, IA, USA.

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http://dx.doi.org/10.1007/978-3-319-46723-8_40DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471813PMC
October 2016

Globally Optimal Label Fusion with Shape Priors.

Med Image Comput Comput Assist Interv 2016 Oct 2;9901:538-546. Epub 2016 Oct 2.

Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, USA.

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http://link.springer.com/10.1007/978-3-319-46723-8_62
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http://dx.doi.org/10.1007/978-3-319-46723-8_62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471814PMC
October 2016

Entropy-based particle correspondence for shape populations.

Int J Comput Assist Radiol Surg 2016 Jul 8;11(7):1221-32. Epub 2015 Dec 8.

University of Utah, Salt Lake City, UT, USA.

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http://dx.doi.org/10.1007/s11548-015-1319-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899300PMC
July 2016

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

Invest Ophthalmol Vis Sci 2016 07;57(9):OCT621-OCT630

Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, Iowa, United States 2Iowa Institute for Biomedical Imaging, The University of Iowa, Iowa City, Iowa, United States.

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http://dx.doi.org/10.1167/iovs.15-18924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215413PMC
July 2016

Enhanced Cortical Thickness Measurements for Rodent Brains via Lagrangian-based RK4 Streamline Computation.

Proc SPIE Int Soc Opt Eng 2016 Feb 21;9784. Epub 2016 Mar 21.

University of North Carolina at Chapel Hill, Department of Computer Science, United States; University of North Carolina at Chapel Hill, Department of Psychiatry, United States.

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http://dx.doi.org/10.1117/12.2216420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825173PMC
February 2016

Effects of prenatal cocaine exposure on early postnatal rodent brain structure and diffusion properties.

Neurotoxicol Teratol 2015 Jan-Feb;47:80-8. Epub 2014 Nov 22.

Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1016/j.ntt.2014.11.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4291294PMC
September 2015

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

Proc SPIE Int Soc Opt Eng 2015;9413

Iowa Institute for Biomedical Imaging, Dept. of Electrical & Computer Engineering, and Ophthalmology & Visual Sciences, The Univ. of Iowa, Iowa City, IA.

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http://dx.doi.org/10.1117/12.2082327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449148PMC
January 2015

Magnetic resonance microscopy-based analyses of the neuroanatomical effects of gestational day 9 ethanol exposure in mice.

Neurotoxicol Teratol 2013 Sep-Oct;39:77-83. Epub 2013 Jul 30.

Bowles Center for Alcohol Studies, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ntt.2013.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795920PMC
November 2014

Robust cortical thickness measurement with LOGISMOS-B.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4324754PMC
http://dx.doi.org/10.1007/978-3-319-10404-1_90DOI Listing
November 2014

Comparison of magnetic resonance imaging in live vs. post mortem rat brains.

PLoS One 2013 13;8(8):e71027. Epub 2013 Aug 13.

University of North Carolina at Chapel Hill, Department of Psychiatry, Chapel Hill, North Carolina, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071027PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742751PMC
May 2014

Particle-guided image registration.

Med Image Comput Comput Assist Interv 2013 ;16(Pt 3):203-10

Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974564PMC
http://dx.doi.org/10.1007/978-3-642-40760-4_26DOI Listing
February 2014

DTIPrep: quality control of diffusion-weighted images.

Front Neuroinform 2014 30;8. Epub 2014 Jan 30.

Department of Psychiatry, University of North Carolina at Chapel Hill Chapel Hill, NC, USA.

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http://journal.frontiersin.org/article/10.3389/fninf.2014.00
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http://dx.doi.org/10.3389/fninf.2014.00004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906573PMC
February 2014

RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI.

J Neurosci Methods 2014 Jan 18;221:175-82. Epub 2013 Oct 18.

The University of Iowa, Department of Electrical and Computer Engineering, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jneumeth.2013.09.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914765PMC
January 2014

Adolescent binge ethanol treatment alters adult brain regional volumes, cortical extracellular matrix protein and behavioral flexibility.

Pharmacol Biochem Behav 2014 Jan 23;116:142-51. Epub 2013 Nov 23.

Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, CB# 7178, Chapel Hill, NC 27599-7178, United States; Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States. Electronic address:

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http://dx.doi.org/10.1016/j.pbb.2013.11.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913047PMC
January 2014

A midas plugin to enable construction of reproducible web-based image processing pipelines.

Front Neuroinform 2013 30;7:46. Epub 2013 Dec 30.

Department of Electrical-Computer Engineering, University of Iowa Iowa City, IA, USA.

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http://dx.doi.org/10.3389/fninf.2013.00046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875239PMC
January 2014

Peri-adolescent ethanol vapor exposure produces reductions in hippocampal volume that are correlated with deficits in prepulse inhibition of the startle.

Alcohol Clin Exp Res 2013 Sep 11;37(9):1466-75. Epub 2013 Apr 11.

Department of Molecular and Cellular Neurosciences , The Scripps Research Institute, La Jolla, California.

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http://dx.doi.org/10.1111/acer.12125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715576PMC
September 2013

Fully automated rodent brain MR image processing pipeline on a Midas server: from acquired images to region-based statistics.

Front Neuroinform 2013 13;7:15. Epub 2013 Aug 13.

Neuro Image Research and Analysis Laboratories, Department of Psychiatry, University of North Carolina Chapel Hill, NC, USA.

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http://dx.doi.org/10.3389/fninf.2013.00015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3741535PMC
August 2013

DTI Quality Control Assessment via Error Estimation From Monte Carlo Simulations.

Proc SPIE Int Soc Opt Eng 2013 Mar;8669:1667549

Dept. of Psychiatry, University of North Carolina, Chapel Hill US.

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http://dx.doi.org/10.1117/12.2006925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702180PMC
March 2013

The translational role of diffusion tensor image analysis in animal models of developmental pathologies.

Dev Neurosci 2012 24;34(1):5-19. Epub 2012 May 24.

Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

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http://dx.doi.org/10.1159/000336825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566876PMC
January 2013

Postnatal day 7 ethanol treatment causes persistent reductions in adult mouse brain volume and cortical neurons with sex specific effects on neurogenesis.

Alcohol 2012 Sep 7;46(6):603-12. Epub 2012 May 7.

Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill CB# 7178, Chapel Hill, NC 27599-7178, USA.

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http://dx.doi.org/10.1016/j.alcohol.2012.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552379PMC
September 2012

MANDIBULAR ASYMMETRY CHARACTERIZATION USING GENERALIZED TENSOR-BASED MORPHOMETRY.

Proc IEEE Int Symp Biomed Imaging 2011 Dec;2011:1175-1178

Department of Psychiatry, University of North Carolina at Chapel Hill.

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http://dx.doi.org/10.1109/ISBI.2011.5872611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892912PMC
December 2011

Use of High Resolution 3D Diffusion Tensor Imaging to Study Brain White Matter Development in Live Neonatal Rats.

Front Psychiatry 2011 10;2:54. Epub 2011 Oct 10.

Department of Radiology, University of North Carolina at Chapel Hill Chapel Hill, NC, USA.

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http://dx.doi.org/10.3389/fpsyt.2011.00054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189600PMC
November 2011

Efficient, Graph-based White Matter Connectivity from Orientation Distribution Functions via Multi-directional Graph Propagation.

Proc SPIE Int Soc Opt Eng 2011 7;7962:79620S. Epub 2011 Mar 7.

Department of Psychiatry, University of North Carolina, Chapel Hill, USA.

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http://dx.doi.org/10.1117/12.878291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468156PMC
March 2011

Automatic Skull-stripping of Rat MRI/DTI Scans and Atlas Building.

Proc SPIE Int Soc Opt Eng 2011 Mar;7962:7962251-7962257

University of North Carolina at Chapel Hill, Department of Psychiatry.

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http://dx.doi.org/10.1117/12.878405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3168953PMC
March 2011

Automatic cortical thickness analysis on rodent brain.

Proc SPIE Int Soc Opt Eng 2011 Mar;7962:7962481-79624811

Department of Computer Science, University of North Carolina, Chapel Hill NC, USA.

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http://dx.doi.org/10.1117/12.878305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3168533PMC
March 2011

Shape-correlated Deformation Statistics for Respiratory Motion Prediction in 4D Lung.

Proc SPIE Int Soc Opt Eng 2010 Feb;7625

Computer Science Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

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http://midag.cs.unc.edu/pubs/papers/spie2010.pdf
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http://proceedings.spiedigitallibrary.org/proceeding.aspx?do
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http://dx.doi.org/10.1117/12.843974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824262PMC
February 2010

Cortical correspondence with probabilistic fiber connectivity.

Inf Process Med Imaging 2009 ;21:651-63

Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2751643PMC
http://dx.doi.org/10.1007/978-3-642-02498-6_54DOI Listing
September 2009

Corpus callosum subdivision based on a probabilistic model of inter-hemispheric connectivity.

Med Image Comput Comput Assist Interv 2005 ;8(Pt 2):765-72

Dept. of Computer Science, Univ. of North Carolina, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1007/11566489_94DOI Listing
June 2006