Brian B Avants

Brian B Avants

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Brian B Avants

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Learning image-based spatial transformations via convolutional neural networks: A review.

Magn Reson Imaging 2019 12 11;64:142-153. Epub 2019 Jun 11.

Department of Radiology, University of Pennsylvania, Philadelphia, PA, United States of America.

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http://dx.doi.org/10.1016/j.mri.2019.05.037DOI Listing
December 2019

Small Animal Multivariate Brain Analysis (SAMBA) - a High Throughput Pipeline with a Validation Framework.

Neuroinformatics 2019 Jul;17(3):451-472

Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC, 27710, USA.

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http://dx.doi.org/10.1007/s12021-018-9410-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584586PMC
July 2019

Multi-template analysis of human perirhinal cortex in brain MRI: Explicitly accounting for anatomical variability.

Neuroimage 2017 01 1;144(Pt A):183-202. Epub 2016 Oct 1.

Penn Image Computing and Science Laboratory (PICSL), Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA; Department of Radiology, University of Pennsylvania, Philadelphia, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2016.09.070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5183532PMC
January 2017

Arterial spin labeling perfusion predicts longitudinal decline in semantic variant primary progressive aphasia.

J Neurol 2016 Oct 5;263(10):1927-38. Epub 2016 Jul 5.

Department of Neurology, Penn Frontotemporal Degeneration Center, University of Pennsylvania Perelman School of Medicine, 3 West Gates, Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1007/s00415-016-8221-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5097861PMC
October 2016

Neuropsychological Testing Predicts Cerebrospinal Fluid Amyloid-β in Mild Cognitive Impairment.

J Alzheimers Dis 2015 ;46(4):901-12

Department of Neurology, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.3233/JAD-142943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4699841PMC
June 2016

High-density three-dimensional localization microscopy across large volumes.

Nat Methods 2016 Apr 7;13(4):359-65. Epub 2016 Mar 7.

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

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http://dx.doi.org/10.1038/nmeth.3797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889433PMC
April 2016

The pediatric template of brain perfusion.

Sci Data 2015 3;2:150003. Epub 2015 Feb 3.

Department of Neurology, University of California , Los Angeles, California 90095, USA.

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http://dx.doi.org/10.1038/sdata.2015.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413243PMC
December 2015

Neuroinformatics and the The Insight ToolKit.

Front Neuroinform 2015 26;9. Epub 2015 Mar 26.

Department of Radiology and Medical Imaging, University of Virginia Charlottesville, VA, USA.

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http://dx.doi.org/10.3389/fninf.2015.00005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374465PMC
April 2015

Eigenanatomy: sparse dimensionality reduction for multi-modal medical image analysis.

Methods 2015 Feb 22;73:43-53. Epub 2014 Oct 22.

Penn Image Computing and Science Laboratory, University of Pennsylvania, Philadelphia, PA, United States; Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, PA, United States.

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http://dx.doi.org/10.1016/j.ymeth.2014.10.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329066PMC
February 2015

Decomposing cerebral blood flow MRI into functional and structural components: a non-local approach based on prediction.

Neuroimage 2015 Jan 1;105:156-70. Epub 2014 Nov 1.

Penn Image Computing and Science Laboratory, University of Pennsylvania, Philadelphia, PA, USA; Department of Radiology, Hospital of the University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2014.10.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356637PMC
January 2015

Relating brain anatomy and cognitive ability using a multivariate multimodal framework.

Neuroimage 2014 Oct 13;99:477-86. Epub 2014 May 13.

Penn Frontotemporal Degeneration Center, Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2014.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151353PMC
October 2014

Subject-specific functional parcellation via prior based eigenanatomy.

Neuroimage 2014 Oct 20;99:14-27. Epub 2014 May 20.

Penn Image Computing and Science Laboratory (PICSL), Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2014.05.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382016PMC
October 2014

Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements.

Neuroimage 2014 Oct 29;99:166-79. Epub 2014 May 29.

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

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http://dx.doi.org/10.1016/j.neuroimage.2014.05.044DOI Listing
October 2014

The power of neuroimaging biomarkers for screening frontotemporal dementia.

Hum Brain Mapp 2014 Sep 31;35(9):4827-40. Epub 2014 Mar 31.

Department of Neurology, Penn Frontotemporal Degeneration Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1002/hbm.22515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107021PMC
September 2014

Genetic and neuroanatomic associations in sporadic frontotemporal lobar degeneration.

Neurobiol Aging 2014 Jun 2;35(6):1473-82. Epub 2013 Dec 2.

Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Penn Frontotemporal Degeneration Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.

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http://dx.doi.org/10.1016/j.neurobiolaging.2013.11.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961542PMC
June 2014

The Insight ToolKit image registration framework.

Front Neuroinform 2014 28;8:44. Epub 2014 Apr 28.

Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania Philadelphia, PA, USA.

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http://dx.doi.org/10.3389/fninf.2014.00044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009425PMC
May 2014

Logical circularity in voxel-based analysis: normalization strategy may induce statistical bias.

Hum Brain Mapp 2014 Mar 14;35(3):745-59. Epub 2012 Nov 14.

Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, Virginia.

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http://dx.doi.org/10.1002/hbm.22211DOI Listing
March 2014

Histology-derived volumetric annotation of the human hippocampal subfields in postmortem MRI.

Neuroimage 2014 Jan 12;84:505-23. Epub 2013 Sep 12.

Penn Image Computing and Science Laboratory (PICSL), Department of Radiology, University of Pennsylvania, 3600 Market Street, Suite 370, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuroimage.2013.08.067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864597PMC
January 2014

Explicit B-spline regularization in diffeomorphic image registration.

Front Neuroinform 2013 23;7:39. Epub 2013 Dec 23.

Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania Philadelphia, PA, USA.

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http://dx.doi.org/10.3389/fninf.2013.00039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870320PMC
January 2014

White matter imaging helps dissociate tau from TDP-43 in frontotemporal lobar degeneration.

J Neurol Neurosurg Psychiatry 2013 Sep 9;84(9):949-55. Epub 2013 Mar 9.

Department of Neurology, Perelman School of Medicine, Frontotemporal Degeneration Center, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://jnnp.bmj.com/cgi/doi/10.1136/jnnp-2012-304418
Publisher Site
http://dx.doi.org/10.1136/jnnp-2012-304418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737288PMC
September 2013

Associations between children's socioeconomic status and prefrontal cortical thickness.

Dev Sci 2013 Sep 30;16(5):641-52. Epub 2013 Jul 30.

Department of Psychology, University of Pennsylvania, USA.

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http://dx.doi.org/10.1111/desc.12096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775298PMC
September 2013

A digital atlas of the dog brain.

PLoS One 2012 20;7(12):e52140. Epub 2012 Dec 20.

Department of Neurology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052140PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527386PMC
June 2013

Regional and hemispheric variation in cortical thickness in chimpanzees (Pan troglodytes).

J Neurosci 2013 Mar;33(12):5241-8

Division on of Developmental and Cognitive Neuroscience, Yerkes National Primate Research Center, Atlanta, GA 30322, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643894PMC
http://dx.doi.org/10.1523/JNEUROSCI.2996-12.2013DOI Listing
March 2013

Robust Automated Amygdala Segmentation via Multi-Atlas Diffeomorphic Registration.

Front Neurosci 2012 29;6:166. Epub 2012 Nov 29.

Department of Psychology, University of Wisconsin-Madison Madison, WI, USA ; Waisman Center, University of Wisconsin-Madison Madison, WI, USA.

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http://dx.doi.org/10.3389/fnins.2012.00166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509347PMC
December 2012

RECONSTRUCTION OF THE HUMAN HIPPOCAMPUS IN 3D FROM HISTOLOGY AND HIGH-RESOLUTION EX-VIVO MRI.

Proc IEEE Int Symp Biomed Imaging 2012 Dec;2012:294-297

Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1109/ISBI.2012.6235542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892900PMC
December 2012

Quantitative mouse brain phenotyping based on single and multispectral MR protocols.

Neuroimage 2012 Nov 23;63(3):1633-45. Epub 2012 Jul 23.

Center for InVivo Microscopy, Box 3302, Duke University Medical Center, Durham, NC 27710, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2012.07.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604698PMC
November 2012

Measuring longitudinal change in the hippocampal formation from in vivo high-resolution T2-weighted MRI.

Neuroimage 2012 Apr 28;60(2):1266-79. Epub 2012 Jan 28.

Penn Image Computing and Science Laboratory-PICSL, Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2012.01.098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667607PMC
April 2012

An open source multivariate framework for n-tissue segmentation with evaluation on public data.

Neuroinformatics 2011 Dec;9(4):381-400

Penn Image Computing and Science Laboratory, University of Pennsylvania, 3600 Market Street, Suite 370, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1007/s12021-011-9109-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297199PMC
December 2011

Ventilation-based segmentation of the lungs using hyperpolarized (3)He MRI.

J Magn Reson Imaging 2011 Oct 11;34(4):831-41. Epub 2011 Aug 11.

Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, Virginia, USA.

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http://doi.wiley.com/10.1002/jmri.22738
Publisher Site
http://dx.doi.org/10.1002/jmri.22738DOI Listing
October 2011

A reproducible evaluation of ANTs similarity metric performance in brain image registration.

Neuroimage 2011 Feb 17;54(3):2033-44. Epub 2010 Sep 17.

Penn Image Computing and Science Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S105381191001206
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http://dx.doi.org/10.1016/j.neuroimage.2010.09.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065962PMC
February 2011

STRUCTURAL CONNECTIVITY VIA THE TENSOR-BASED MORPHOMETRY.

Proc IEEE Int Symp Biomed Imaging 2011

Department of Brain and Cognitive Sciences, Seoul National University, Korea.

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http://dx.doi.org/10.1109/ISBI.2011.5872528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811040PMC
January 2011

Nearly automatic segmentation of hippocampal subfields in in vivo focal T2-weighted MRI.

Neuroimage 2010 Dec 30;53(4):1208-24. Epub 2010 Jun 30.

Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2010.06.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939190PMC
December 2010

Estimation of perfusion and arterial transit time in myocardium using free-breathing myocardial arterial spin labeling with navigator-echo.

Magn Reson Med 2010 Nov;64(5):1289-95

Department of Neurology, Ahmanson-Lovelace Brain Mapping Center, University of California at Los Angeles, Los Angeles, California 90095-7085, USA.

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http://dx.doi.org/10.1002/mrm.22630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965813PMC
November 2010

N4ITK: improved N3 bias correction.

IEEE Trans Med Imaging 2010 Jun 8;29(6):1310-20. Epub 2010 Apr 8.

Department of Radiology, University of Pennsylvania, Philadelphia, PA 19140, USA.

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http://dx.doi.org/10.1109/TMI.2010.2046908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071855PMC
June 2010

The optimal template effect in hippocampus studies of diseased populations.

Neuroimage 2010 Feb 8;49(3):2457-66. Epub 2009 Oct 8.

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

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http://dx.doi.org/10.1016/j.neuroimage.2009.09.062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818274PMC
February 2010

Appearance and incomplete label matching for diffeomorphic template based hippocampus segmentation.

Hippocampus 2009 Jun;19(6):565-71

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

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http://dx.doi.org/10.1002/hipo.20619DOI Listing
June 2009

Structure specific analysis of the hippocampus in temporal lobe epilepsy.

Hippocampus 2009 Jun;19(6):517-25

Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1002/hipo.20620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2893564PMC
June 2009

Registration based cortical thickness measurement.

Neuroimage 2009 Apr 25;45(3):867-79. Epub 2008 Dec 25.

Department of Radiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2008.12.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836782PMC
April 2009

Directly manipulated free-form deformation image registration.

IEEE Trans Image Process 2009 Mar 20;18(3):624-35. Epub 2009 Jan 20.

Penn Image Computing and Science Lab, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104-2644, USA.

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http://ieeexplore.ieee.org/iel5/83/4782056/04757202.pdf?arnu
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http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumbe
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http://dx.doi.org/10.1109/TIP.2008.2010072DOI Listing
March 2009

A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T.

Neuroimage 2009 Jan 18;44(2):385-98. Epub 2008 Sep 18.

Penn Image Computing and Science Laboratory (PICSL), Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1016/j.neuroimage.2008.08.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2650508PMC
January 2009

Shape-based alignment of hippocampal subfields: evaluation in postmortem MRI.

Med Image Comput Comput Assist Interv 2008 ;11(Pt 1):510-7

Department of Radiology, University of Pennsylvania, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680118PMC
http://dx.doi.org/10.1007/978-3-540-85988-8_61DOI Listing
December 2008

Cardiac medial modeling and time-course heart wall thickness analysis.

Med Image Comput Comput Assist Interv 2008 ;11(Pt 2):766-73

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

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http://dx.doi.org/10.1007/978-3-540-85990-1_92DOI Listing
December 2008

Altered resting cerebral blood flow in adolescents with in utero cocaine exposure revealed by perfusion functional MRI.

Pediatrics 2007 Nov;120(5):e1245-54

Department of Radiology and Neurology, Center for Functional Neuroimaging, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1542/peds.2006-2596DOI Listing
November 2007

Effects of heavy in utero cocaine exposure on adolescent caudate morphology.

Pediatr Neurol 2007 Oct;37(4):275-9

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

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http://dx.doi.org/10.1016/j.pediatrneurol.2007.06.012DOI Listing
October 2007

Multivariate examination of brain abnormality using both structural and functional MRI.

Neuroimage 2007 Jul 19;36(4):1189-99. Epub 2007 Apr 19.

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

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http://dx.doi.org/10.1016/j.neuroimage.2007.04.009DOI Listing
July 2007

Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex.

Med Image Anal 2006 Jun 3;10(3):397-412. Epub 2005 Jun 3.

Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104-6389, USA.

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http://dx.doi.org/10.1016/j.media.2005.03.005DOI Listing
June 2006

Towards a dynamic model of pulmonary parenchymal deformation: evaluation of methods for temporal reparameterization of lung data.

Med Image Comput Comput Assist Interv 2005 ;8(Pt 2):328-35

University of Pennsylvania, Philadelphia PA 19104, USA.

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http://dx.doi.org/10.1007/11566489_41DOI Listing
June 2006