Research Group: Intelligent Medical Imaging Research Group

Dr. Gholipour develops technology, knowledge, and resources for in-vivo analysis of normal and abnormal brain growth before and early after birth when the brain undergoes its most rapid formative growth. These technologies, developed for computational developmental neuroscience and neurology, have enabled advanced studies into characterizing the structure and function of the early developing brain and the mechanism and patterns of altered brain development.



Ali Gholipour is an Assistant Professor in Radiology at Harvard Medical School, principal investigator and director of the Intelligent Medical Imaging research group at the Computational Radiology Laboratory, and the Director of Translational Research in the Radiology Department at Boston Children’s Hospital. He received all his degrees in Electrical Engineering (PhD’08 at the Univ. of Texas at Dallas, and MS’03, BS’01 at the Univ. of Tehran) and is currently a Senior Member of the IEEE. With long-term research interests in signal and image processing and intelligent systems, he has turned his focus to machine learning and medical imaging in the past decade. Dr. Gholipour is the recipient of awards from the Thrasher Research Fund, the Harvard Clinical and Translational Science Center, the McKnight Foundation, Fetal Health Foundation, and the Office of Faculty Development at Boston Children's Hospital (Eleanor and Miles Shore Fellowship); and is principal investigator on a number of projects funded by the National Institutes of Health.


Publications powered by Harvard Catalyst Profiles

  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  8. Gholipour A, Warfield SK. Motion-corrected foetal cardiac MRI. Nat Biomed Eng. 2019 11; 3(11):852-854. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  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. View abstract
  46. 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. View abstract
  47. 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. View abstract
  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. View abstract
  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. View abstract
  50. 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. View abstract
  51. 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 abstract
  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 abstract
  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. View abstract
  54. 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. View abstract
  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. View abstract
  56. 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 abstract
  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. View abstract