Harvard Catalyst Profiles

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Ali Gholipour-Baboli, Ph.D.

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The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01NS106030 (GHOLIPOUR-BABOLI, ALI) Feb 15, 2019 - Jan 31, 2024
    Advancing microstructural and vascular neuroimaging in perinatal stroke
    Role: Principal Investigator
  2. R01EB018988 (GHOLIPOUR-BABOLI, ALI) Jul 1, 2014 - Jun 30, 2018
    Motion-robust super-resolution diffusion weighted MRI of early brain development
    Role: Principal Investigator
  3. R03DE022109 (GHOLIPOUR-BABOLI, ALI) Jul 1, 2011 - Jun 30, 2014
    Super-resolution Reconstruction of Fetal Craniofacial MRI
    Role: Principal Investigator

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Singh A, Salehi SSM, Gholipour A. Deep Predictive Motion Tracking in Magnetic Resonance Imaging: Application to Fetal Imaging. IEEE Trans Med Imaging. 2020 Nov; 39(11):3523-3534. PMID: 32746102.
    Citations:    Fields:    
  2. Jaimes C, Rofeberg V, Stopp C, Ortinau CM, Gholipour A, Friedman KG, Tworetzky W, Estroff J, Newburger JW, Wypij D, Warfield SK, Yang E, Rollins CK. Association of Isolated Congenital Heart Disease with Fetal Brain Maturation. AJNR Am J Neuroradiol. 2020 08; 41(8):1525-1531. PMID: 32646947.
    Citations:    Fields:    
  3. Vasung L, Rollins CK, Velasco-Annis C, Yun HJ, Zhang J, Warfield SK, Feldman HA, Gholipour A, Grant PE. Spatiotemporal Differences in the Regional Cortical Plate and Subplate Volume Growth during Fetal Development. Cereb Cortex. 2020 Jun 30; 30(8):4438-4453. PMID: 32147720.
    Citations:    Fields:    
  4. Karimi D, Dou H, Warfield SK, Gholipour A. Deep learning with noisy labels: Exploring techniques and remedies in medical image analysis. Med Image Anal. 2020 10; 65:101759. PMID: 32623277.
    Citations: 2     Fields:    
  5. Afacan O, Hoge WS, Wallace TE, Gholipour A, Kurugol S, Warfield SK. Simultaneous Motion and Distortion Correction Using Dual-Echo Diffusion-Weighted MRI. J Neuroimaging. 2020 05; 30(3):276-285. PMID: 32374453.
    Citations:    Fields:    
  6. Jaimes C, Machado-Rivas F, Afacan O, Khan S, Marami B, Ortinau CM, Rollins CK, Velasco-Annis C, Warfield SK, Gholipour A. In vivo characterization of emerging white matter microstructure in the fetal brain in the third trimester. Hum Brain Mapp. 2020 Aug 15; 41(12):3177-3185. PMID: 32374063.
    Citations: 1     Fields:    
  7. Vasung L, Rollins CK, Yun HJ, Velasco-Annis C, Zhang J, Wagstyl K, Evans A, Warfield SK, Feldman HA, Grant PE, Gholipour A. Quantitative In vivo MRI Assessment of Structural Asymmetries and Sexual Dimorphism of Transient Fetal Compartments in the Human Brain. Cereb Cortex. 2020 03 14; 30(3):1752-1767. PMID: 31602456.
    Citations: 2     Fields:    
  8. Gholipour A, Warfield SK. Motion-corrected foetal cardiac MRI. Nat Biomed Eng. 2019 11; 3(11):852-854. PMID: 31645682.
    Citations:    Fields:    Translation:Humans
  9. Sui Y, Afacan O, Gholipour A, Warfield SK. Isotropic MRI Super-Resolution Reconstruction with Multi-scale Gradient Field Prior. Med Image Comput Comput Assist Interv. 2019 Oct; 11766:3-11. PMID: 32832937.
    Citations:    Fields:    
  10. Afacan O, Estroff JA, Yang E, Barnewolt CE, Connolly SA, Parad RB, Mulkern RV, Warfield SK, Gholipour A. Fetal Echoplanar Imaging: Promises and Challenges. Top Magn Reson Imaging. 2019 Oct; 28(5):245-254. PMID: 31592991.
    Citations:    Fields:    Translation:Humans
  11. Ortinau CM, Rollins CK, Gholipour A, Yun HJ, Marshall M, Gagoski B, Afacan O, Friedman K, Tworetzky W, Warfield SK, Newburger JW, Inder TE, Grant PE, Im K. Early-Emerging Sulcal Patterns Are Atypical in Fetuses with Congenital Heart Disease. Cereb Cortex. 2019 07 22; 29(8):3605-3616. PMID: 30272144.
    Citations: 3     Fields:    Translation:Humans
  12. Sourati J, Gholipour A, Dy JG, Tomas-Fernandez X, Kurugol S, Warfield SK. Intelligent Labeling Based on Fisher Information for Medical Image Segmentation Using Deep Learning. IEEE Trans Med Imaging. 2019 11; 38(11):2642-2653. PMID: 30932833.
    Citations:    Fields:    Translation:Humans
  13. Enguehard J, O'Halloran P, Gholipour A. Semi Supervised Learning with Deep Embedded Clustering for Image Classification and Segmentation. IEEE Access. 2019; 7:11093-11104. PMID: 31588387.
    Citations: 1     
  14. Hashemi SR, Salehi SSM, Erdogmus D, Prabhu SP, Warfield SK, Gholipour A. Asymmetric Loss Functions and Deep Densely Connected Networks for Highly Imbalanced Medical Image Segmentation: Application to Multiple Sclerosis Lesion Detection. IEEE Access. 2019; 7:721-1735. PMID: 31528523.
    Citations: 2     
  15. Marami B, Scherrer B, Khan S, Afacan O, Prabhu SP, Sahin M, Warfield SK, Gholipour A. Motion-robust diffusion compartment imaging using simultaneous multi-slice acquisition. Magn Reson Med. 2019 05; 81(5):3314-3329. PMID: 30443929.
    Citations:    Fields:    Translation:Humans
  16. Ortinau CM, Mangin-Heimos K, Moen J, Alexopoulos D, Inder TE, Gholipour A, Shimony JS, Eghtesady P, Schlaggar BL, Smyser CD. Prenatal to postnatal trajectory of brain growth in complex congenital heart disease. Neuroimage Clin. 2018; 20:913-922. PMID: 30308377.
    Citations: 2     Fields:    Translation:Humans
  17. Sourati J, Gholipour A, Dy JG, Kurugol S, Warfield SK. Active Deep Learning with Fisher Information for Patch-wise Semantic Segmentation. Deep Learn Med Image Anal Multimodal Learn Clin Decis Support (2018). 2018 Sep; 11045:83-91. PMID: 30450490.
    Citations: 3     
  18. Khan S, Vasung L, Marami B, Rollins CK, Afacan O, Ortinau CM, Yang E, Warfield SK, Gholipour A. Fetal brain growth portrayed by a spatiotemporal diffusion tensor MRI atlas computed from in utero images. Neuroimage. 2019 01 15; 185:593-608. PMID: 30172006.
    Citations: 6     Fields:    Translation:Humans
  19. Mohseni Salehi SS, Khan S, Erdogmus D, Gholipour A. Real-Time Deep Pose Estimation With Geodesic Loss for Image-to-Template Rigid Registration. IEEE Trans Med Imaging. 2019 02; 38(2):470-481. PMID: 30138909.
    Citations: 1     Fields:    Translation:Humans
  20. Benali S, Johnston PR, Gholipour A, Dugan ME, Heberlein K, Bhat H, Bixby SD. Simultaneous multi-slice accelerated turbo spin echo of the knee in pediatric patients. Skeletal Radiol. 2018 Jun; 47(6):821-831. PMID: 29332200.
    Citations: 1     Fields:    Translation:Humans
  21. Kurugol S, Marami B, Afacan O, Warfield SK, Gholipour A. Motion-Robust Spatially Constrained Parameter Estimation in Renal Diffusion-Weighted MRI by 3D Motion Tracking and Correction of Sequential Slices. Mol Imaging Reconstr Anal Mov Body Organs Stroke Imaging Treat (2017). 2017; 10555:75-85. PMID: 29457154.
    Citations: 1     
  22. Mohseni Salehi SS, Erdogmus D, Gholipour A. Auto-Context Convolutional Neural Network (Auto-Net) for Brain Extraction in Magnetic Resonance Imaging. IEEE Trans Med Imaging. 2017 11; 36(11):2319-2330. PMID: 28678704.
    Citations: 11     Fields:    Translation:Humans
  23. Marami B, Mohseni Salehi SS, Afacan O, Scherrer B, Rollins CK, Yang E, Estroff JA, Warfield SK, Gholipour A. Temporal slice registration and robust diffusion-tensor reconstruction for improved fetal brain structural connectivity analysis. Neuroimage. 2017 08 01; 156:475-488. PMID: 28433624.
    Citations: 12     Fields:    Translation:Humans
  24. Tourbier S, Velasco-Annis C, Taimouri V, Hagmann P, Meuli R, Warfield SK, Bach Cuadra M, Gholipour A. Automated template-based brain localization and extraction for fetal brain MRI reconstruction. Neuroimage. 2017 07 15; 155:460-472. PMID: 28408290.
    Citations: 2     Fields:    Translation:Humans
  25. Gholipour A, Rollins CK, Velasco-Annis C, Ouaalam A, Akhondi-Asl A, Afacan O, Ortinau CM, Clancy S, Limperopoulos C, Yang E, Estroff JA, Warfield SK. A normative spatiotemporal MRI atlas of the fetal brain for automatic segmentation and analysis of early brain growth. Sci Rep. 2017 03 28; 7(1):476. PMID: 28352082.
    Citations: 14     Fields:    Translation:Humans
  26. Jia Y, Gholipour A, He Z, Warfield SK. A New Sparse Representation Framework for Reconstruction of an Isotropic High Spatial Resolution MR Volume From Orthogonal Anisotropic Resolution Scans. IEEE Trans Med Imaging. 2017 05; 36(5):1182-1193. PMID: 28129152.
    Citations:    Fields:    Translation:Humans
  27. Marami B, Scherrer B, Afacan O, Warfield SK, Gholipour A. Motion-Robust Reconstruction based on Simultaneous Multi-Slice Registration for Diffusion-Weighted MRI of Moving Subjects. Med Image Comput Comput Assist Interv. 2016 Oct; 9902:544-552. PMID: 28127590.
    Citations: 3     Fields:    Translation:Humans
  28. Marami B, Scherrer B, Afacan O, Erem B, Warfield SK, Gholipour A. Motion-Robust Diffusion-Weighted Brain MRI Reconstruction Through Slice-Level Registration-Based Motion Tracking. IEEE Trans Med Imaging. 2016 10; 35(10):2258-2269. PMID: 27834639.
    Citations: 5     Fields:    Translation:Humans
  29. Afacan O, Gholipour A, Mulkern RV, Barnewolt CE, Estroff JA, Connolly SA, Parad RB, Bairdain S, Warfield SK. Fetal lung apparent diffusion coefficient measurement using diffusion-weighted MRI at 3 Tesla: Correlation with gestational age. J Magn Reson Imaging. 2016 12; 44(6):1650-1655. PMID: 27159847.
    Citations: 2     Fields:    Translation:HumansCells
  30. Pier DB, Gholipour A, Afacan O, Velasco-Annis C, Clancy S, Kapur K, Estroff JA, Warfield SK. 3D Super-Resolution Motion-Corrected MRI: Validation of Fetal Posterior Fossa Measurements. J Neuroimaging. 2016 09; 26(5):539-44. PMID: 26990618.
    Citations:    Fields:    Translation:Humans
  31. Gholipour A, Afacan O, Aganj I, Scherrer B, Prabhu SP, Sahin M, Warfield SK. Super-resolution reconstruction in frequency, image, and wavelet domains to reduce through-plane partial voluming in MRI. Med Phys. 2015 Dec; 42(12):6919-32. PMID: 26632048.
    Citations: 4     Fields:    Translation:Humans
  32. Jia Y, He Z, Gholipour A, Warfield SK. Single Anisotropic 3-D MR Image Upsampling via Overcomplete Dictionary Trained From In-Plane High Resolution Slices. IEEE J Biomed Health Inform. 2016 11; 20(6):1552-1561. PMID: 26302522.
    Citations: 1     Fields:    Translation:Humans
  33. Velasco-Annis C, Gholipour A, Afacan O, Prabhu SP, Estroff JA, Warfield SK. Normative biometrics for fetal ocular growth using volumetric MRI reconstruction. Prenat Diagn. 2015 Apr; 35(4):400-8. PMID: 25601041.
    Citations: 2     Fields:    Translation:Humans
  34. Scherrer B, Afacan O, Taquet M, Prabhu SP, Gholipour A, Warfield SK. Accelerated High Spatial Resolution Diffusion-Weighted Imaging. Inf Process Med Imaging. 2015; 24:69-81. PMID: 26167096.
    Citations: 3     Fields:    Translation:Humans
  35. Gholipour A, Lee EY, Warfield SK. The anatomy and art of writing a successful grant application: a practical step-by-step approach. Pediatr Radiol. 2014 Dec; 44(12):1512-7. PMID: 25408133.
    Citations: 1     Fields:    Translation:Humans
  36. Gholipour A, Estroff JA, Barnewolt CE, Robertson RL, Grant PE, Gagoski B, Warfield SK, Afacan O, Connolly SA, Neil JJ, Wolfberg A, Mulkern RV. Fetal MRI: A Technical Update with Educational Aspirations. Concepts Magn Reson Part A Bridg Educ Res. 2014 Nov; 43(6):237-266. PMID: 26225129.
    Citations: 17     
  37. Gholipour A, Limperopoulos C, Clancy S, Clouchoux C, Akhondi-Asl A, Estroff JA, Warfield SK. Construction of a deformable spatiotemporal MRI atlas of the fetal brain: evaluation of similarity metrics and deformation models. Med Image Comput Comput Assist Interv. 2014; 17(Pt 2):292-9. PMID: 25485391.
    Citations: 10     Fields:    Translation:Humans
  38. Clouchoux C, du Plessis AJ, Bouyssi-Kobar M, Tworetzky W, McElhinney DB, Brown DW, Gholipour A, Kudelski D, Warfield SK, McCarter RJ, Robertson RL, Evans AC, Newburger JW, Limperopoulos C. Delayed cortical development in fetuses with complex congenital heart disease. Cereb Cortex. 2013 Dec; 23(12):2932-43. PMID: 22977063.
    Citations: 58     Fields:    Translation:Humans
  39. Scherrer B, Gholipour A, Warfield SK. Super-resolution reconstruction to increase the spatial resolution of diffusion weighted images from orthogonal anisotropic acquisitions. Med Image Anal. 2012 Oct; 16(7):1465-76. PMID: 22770597.
    Citations: 31     Fields:    Translation:HumansCells
  40. Gholipour A, Akhondi-Asl A, Estroff JA, Warfield SK. Multi-atlas multi-shape segmentation of fetal brain MRI for volumetric and morphometric analysis of ventriculomegaly. Neuroimage. 2012 Apr 15; 60(3):1819-31. PMID: 22500924.
    Citations: 24     Fields:    Translation:Humans
  41. Scherrer B, Gholipour A, Warfield SK. Super-Resolution Reconstruction of Diffusion-Weighted Images from Distortion Compensated Orthogonal Anisotropic Acquisitions. Proc Workshop Math Methods Biomed Image Analysis. 2012 Jan; 2012:249-254. PMID: 25356442.
  42. Clouchoux C, Kudelski D, Gholipour A, Warfield SK, Viseur S, Bouyssi-Kobar M, Mari JL, Evans AC, du Plessis AJ, Limperopoulos C. Quantitative in vivo MRI measurement of cortical development in the fetus. Brain Struct Funct. 2012 Jan; 217(1):127-39. PMID: 21562906.
    Citations: 41     Fields:    Translation:Humans
  43. Yousefi S, Kehtarnavaz N, Gholipour A. Improved labeling of subcortical brain structures in atlas-based segmentation of magnetic resonance images. IEEE Trans Biomed Eng. 2012 Jul; 59(7):1808-17. PMID: 21382762.
    Citations: 4     Fields:    Translation:Humans
  44. Scherrer B, Gholipour A, Warfield SK. Super-resolution in diffusion-weighted imaging. Med Image Comput Comput Assist Interv. 2011; 14(Pt 2):124-32. PMID: 21995021.
    Citations: 6     Fields:    Translation:HumansCells
  45. Gholipour A, Polak M, van der Kouwe A, Nevo E, Warfield SK. Motion-robust MRI through real-time motion tracking and retrospective super-resolution volume reconstruction. Annu Int Conf IEEE Eng Med Biol Soc. 2011; 2011:5722-5. PMID: 22255639.
    Citations: 4     Translation:Humans
  46. Yousefi S, Kehtarnavaz N, Gholipour A. Synthesis of cervical tissue second harmonic generation images using Markov random field modeling. Annu Int Conf IEEE Eng Med Biol Soc. 2011; 2011:6180-3. PMID: 22255750.
    Citations:    Translation:HumansAnimals
  47. Gholipour A, Kehtarnavaz N, Scherrer B, Warfield SK. On the accuracy of unwarping techniques for the correction of susceptibility-induced geometric distortion in magnetic resonance Echo-planar images. Annu Int Conf IEEE Eng Med Biol Soc. 2011; 2011:6997-7000. PMID: 22255949.
    Citations: 7     Translation:Humans
  48. Gholipour A, Estroff JA, Barnewolt CE, Connolly SA, Warfield SK. Fetal brain volumetry through MRI volumetric reconstruction and segmentation. Int J Comput Assist Radiol Surg. 2011 May; 6(3):329-39. PMID: 20625848.
    Citations: 15     Fields:    Translation:Humans
  49. Gholipour A, Estroff JA, Warfield SK. Robust super-resolution volume reconstruction from slice acquisitions: application to fetal brain MRI. IEEE Trans Med Imaging. 2010 Oct; 29(10):1739-58. PMID: 20529730.
    Citations: 62     Fields:    Translation:Humans
  50. Gholipour A, Kehtarnavaz N, Yousefi S, Gopinath K, Briggs R. Symmetric deformable image registration via optimization of information theoretic measures. Journal of Image and Vision Computing. 2010; 28(6):965-975. View Publication.
  51. Gholipour A, Estroff JA, Sahin M, Prabhu SP, Warfield SK. Maximum a posteriori estimation of isotropic high-resolution volumetric MRI from orthogonal thick-slice scans. Med Image Comput Comput Assist Interv. 2010; 13(Pt 2):109-16. PMID: 20879305.
    Citations: 10     Fields:    Translation:Humans
  52. Gholipour A, Warfield S. Super-resolution reconstruction of fetal brain MRI. Proc. MICCAI Workshop on Image Analysis for the Developing Brain (IADB’2009). 2009; 45–52. View Publication.
  53. Gholipour A, Kehtarnavaz N, Briggs RW, Gopinath KS, Ringe W, Whittemore A, Cheshkov S, Bakhadirov K. Validation of non-rigid registration between functional and anatomical magnetic resonance brain images. IEEE Trans Biomed Eng. 2008 Feb; 55(2 Pt 1):563-71. PMID: 18269991.
    Citations: 4     Fields:    Translation:Humans
  54. Gholipour A, Kehtarnavaz N, Gopinath K, Briggs R. Cross-validation of deformable registration with field maps in functional magnetic resonance brain imaging. IEEE Journal of Selected Topics in Signal Processing. 2008; 2(6):854-869. View Publication.
  55. Tsang O, Gholipour A, Kehtarnavaz N, Gopinath K, Briggs R, Panahi I. Comparison of tissue segmentation algorithms in neuroimage analysis software tools. Annu Int Conf IEEE Eng Med Biol Soc. 2008; 2008:3924-8. PMID: 19163571.
    Citations: 15     Translation:Humans
  56. Gholipour A, Kehtarnavaz N, Gopinath K, Briggs R, Panahi I. Average field map image template for Echo-Planar image analysis. Annu Int Conf IEEE Eng Med Biol Soc. 2008; 2008:94-7. PMID: 19162602.
    Citations: 15     
  57. Gholipour A, Kehtarnavaz N, Briggs R, Devous M, Gopinath K. Brain functional localization: a survey of image registration techniques. IEEE Trans Med Imaging. 2007 Apr; 26(4):427-51. PMID: 17427731.
    Citations: 51     Fields:    Translation:Humans
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.