Harvard Catalyst Profiles

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Lilla Zollei, Ph.D.



Available: 12/01/22, Expires: 09/01/23

We have student project opportunities in several areas. Some examples are as follows: * manual labeling of anatomical regions of interest * manual labeling of white matter fiber bundles * MRI / histology / OCT image processing * automated tractography comparison between different tools * large invivo MRI data cohort analysis * high resolution postmortem data analysis

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. R21HD106038 (WANG, HUI) Aug 3, 2021 - Jun 30, 2023
    Developmental sensorimotor and cognitive pathways in infant cerebellum with multi-scale imaging
    Role: Co-Principal Investigator
  2. R01HD102616 (ZOLLEI, LILLA) May 1, 2021 - Apr 30, 2026
    Brainstem Arousal Network in Human Consciousness: Healthy development vs SIDS
    Role: Principal Investigator
  3. 2020A011102 (ZOLLEI, LILLA) Mar 1, 2021 - Feb 28, 2023
    American Sudden Infant Death Syndrome Institute, Inc.
    Brainstem Connectivity in Human Consciousness: Healthy development vs SIDS
    Role: Principal Investigator
  4. R21HD095338 (ZOLLEI, LILLA) Apr 1, 2018 - Mar 31, 2021
    Ontogeny of Brainstem Arousal Networks in Human Consciousness
    Role: Principal Investigator
  5. R03EB022754 (ZOLLEI, LILLA) Apr 1, 2017 - Jan 31, 2020
    Development of cortical surface based tools for healthy control infants
    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. Ahtam B, Turesky TK, Zöllei L, Standish J, Grant PE, Gaab N, Im K. Intergenerational Transmission of Cortical Sulcal Patterns from Mothers to their Children. Cereb Cortex. 2021 03 05; 31(4):1888-1897. PMID: 33230560; PMCID: PMC7945013.
    Citations:    Fields:    Translation:Humans
  2. Terrier LM, Hadjikhani N, Velut S, Magnain C, Amelot A, Bernard F, Zöllei L, Destrieux C. The trigeminal system: The meningovascular complex- A review. J Anat. 2021 07; 239(1):1-11. PMID: 33604906.
    Citations: 3     Fields:    Translation:Humans
  3. Jeong H, Ntolkeras G, Alhilani M, Atefi SR, Zöllei L, Fujimoto K, Pourvaziri A, Lev MH, Grant PE, Bonmassar G. Development, validation, and pilot MRI safety study of a high-resolution, open source, whole body pediatric numerical simulation model. PLoS One. 2021; 16(1):e0241682. PMID: 33439896.
    Citations: 1     Fields:    Translation:HumansCTClinical Trials
  4. Warton FL, Taylor PA, Warton CMR, Molteno CD, Wintermark P, Zöllei L, van der Kouwe AJ, Jacobson JL, Jacobson SW, Meintjes EM. Reduced fractional anisotropy in projection, association, and commissural fiber networks in neonates with prenatal methamphetamine exposure. Dev Neurobiol. 2020 11; 80(11-12):381-398. PMID: 33010114.
    Citations: 1     Fields:    Translation:Humans
  5. Cheng J, Dalca AV, Fischl B, Zöllei L. Cortical surface registration using unsupervised learning. Neuroimage. 2020 11 01; 221:117161. PMID: 32702486; PMCID: PMC7784120.
    Citations: 3     Fields:    Translation:Humans
  6. Zöllei L, Iglesias JE, Ou Y, Grant PE, Fischl B. Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0-2 years. Neuroimage. 2020 09; 218:116946. PMID: 32442637.
    Citations: 20     Fields:    Translation:HumansCells
  7. Turesky T, Xie W, Kumar S, Sliva DD, Gagoski B, Vaughn J, Zöllei L, Haque R, Kakon SH, Islam N, Petri WA, Nelson CA, Gaab N. Relating anthropometric indicators to brain structure in 2-month-old Bangladeshi infants growing up in poverty: A pilot study. Neuroimage. 2020 04 15; 210:116540. PMID: 31945509.
    Citations: 3     Fields:    Translation:Humans
  8. Turesky TK, Jensen SKG, Yu X, Kumar S, Wang Y, Sliva DD, Gagoski B, Sanfilippo J, Zöllei L, Boyd E, Haque R, Hafiz Kakon S, Islam N, Petri WA, Nelson CA, Gaab N. The relationship between biological and psychosocial risk factors and resting-state functional connectivity in 2-month-old Bangladeshi infants: A feasibility and pilot study. Dev Sci. 2019 09; 22(5):e12841. PMID: 31016808.
    Citations: 10     Fields:    Translation:Humans
  9. Zöllei L, Jaimes C, Saliba E, Grant PE, Yendiki A. TRActs constrained by UnderLying INfant anatomy (TRACULInA): An automated probabilistic tractography tool with anatomical priors for use in the newborn brain. Neuroimage. 2019 10 01; 199:1-17. PMID: 31132451.
    Citations: 8     Fields:    Translation:Humans
  10. Cohen MA, Dilks DD, Koldewyn K, Weigelt S, Feather J, Kell AJ, Keil B, Fischl B, Zöllei L, Wald L, Saxe R, Kanwisher N. Representational similarity precedes category selectivity in the developing ventral visual pathway. Neuroimage. 2019 08 15; 197:565-574. PMID: 31077844; PMCID: PMC6684321.
    Citations: 6     Fields:    Translation:Humans
  11. Ferradal SL, Gagoski B, Jaimes C, Yi F, Carruthers C, Vu C, Litt JS, Larsen R, Sutton B, Grant PE, Zöllei L. System-Specific Patterns of Thalamocortical Connectivity in Early Brain Development as Revealed by Structural and Functional MRI. Cereb Cortex. 2019 03 01; 29(3):1218-1229. PMID: 29425270; PMCID: PMC6499009.
    Citations: 9     Fields:    Translation:Humans
  12. Ou Y, Zöllei L, Da X, Retzepi K, Murphy SN, Gerstner ER, Rosen BR, Grant PE, Kalpathy-Cramer J, Gollub RL. Field of View Normalization in Multi-Site Brain MRI. Neuroinformatics. 2018 10; 16(3-4):431-444. PMID: 29353341.
    Citations: 8     Fields:    Translation:Humans
  13. Harms MP, Somerville LH, Ances BM, Andersson J, Barch DM, Bastiani M, Bookheimer SY, Brown TB, Buckner RL, Burgess GC, Coalson TS, Chappell MA, Dapretto M, Douaud G, Fischl B, Glasser MF, Greve DN, Hodge C, Jamison KW, Jbabdi S, Kandala S, Li X, Mair RW, Mangia S, Marcus D, Mascali D, Moeller S, Nichols TE, Robinson EC, Salat DH, Smith SM, Sotiropoulos SN, Terpstra M, Thomas KM, Tisdall MD, Ugurbil K, van der Kouwe A, Woods RP, Zöllei L, Van Essen DC, Yacoub E. Extending the Human Connectome Project across ages: Imaging protocols for the Lifespan Development and Aging projects. Neuroimage. 2018 12; 183:972-984. PMID: 30261308; PMCID: PMC6484842.
    Citations: 60     Fields:    Translation:Humans
  14. Edlow BL, Keene CD, Perl DP, Iacono D, Folkerth RD, Stewart W, Mac Donald CL, Augustinack J, Diaz-Arrastia R, Estrada C, Flannery E, Gordon WA, Grabowski TJ, Hansen K, Hoffman J, Kroenke C, Larson EB, Lee P, Mareyam A, McNab JA, McPhee J, Moreau AL, Renz A, Richmire K, Stevens A, Tang CY, Tirrell LS, Trittschuh EH, van der Kouwe A, Varjabedian A, Wald LL, Wu O, Yendiki A, Young L, Zöllei L, Fischl B, Crane PK, Dams-O'Connor K. Multimodal Characterization of the Late Effects of Traumatic Brain Injury: A Methodological Overview of the Late Effects of Traumatic Brain Injury Project. J Neurotrauma. 2018 07 15; 35(14):1604-1619. PMID: 29421973.
    Citations: 14     Fields:    Translation:Humans
  15. Jaimes C, Cheng HH, Soul J, Ferradal S, Rathi Y, Gagoski B, Newburger JW, Grant PE, Zöllei L. Probabilistic tractography-based thalamic parcellation in healthy newborns and newborns with congenital heart disease. J Magn Reson Imaging. 2018 06; 47(6):1626-1637. PMID: 29080379.
    Citations: 4     Fields:    Translation:Humans
  16. Warton FL, Taylor PA, Warton CMR, Molteno CD, Wintermark P, Lindinger NM, Zöllei L, van der Kouwe A, Jacobson JL, Jacobson SW, Meintjes EM. Prenatal methamphetamine exposure is associated with corticostriatal white matter changes in neonates. Metab Brain Dis. 2018 04; 33(2):507-522. PMID: 29063448.
    Citations: 7     Fields:    Translation:Humans
  17. Warton FL, Meintjes EM, Warton CMR, Molteno CD, Lindinger NM, Carter RC, Zöllei L, Wintermark P, Jacobson JL, van der Kouwe A, Jacobson SW. Prenatal methamphetamine exposure is associated with reduced subcortical volumes in neonates. Neurotoxicol Teratol. 2018 Jan - Feb; 65:51-59. PMID: 29069607.
    Citations: 6     Fields:    Translation:Humans
  18. Papadelis C, Butler EE, Rubenstein M, Sun L, Zollei L, Nimec D, Snyder B, Grant PE. Reorganization of the somatosensory cortex in hemiplegic cerebral palsy associated with impaired sensory tracts. Neuroimage Clin. 2018; 17:198-212. PMID: 29159037.
    Citations: 16     Fields:    Translation:Humans
  19. Jacobson SW, Jacobson JL, Molteno CD, Warton CMR, Wintermark P, Hoyme HE, De Jong G, Taylor P, Warton F, Lindinger NM, Carter RC, Dodge NC, Grant E, Warfield SK, Zöllei L, van der Kouwe AJW, Meintjes EM. Heavy Prenatal Alcohol Exposure is Related to Smaller Corpus Callosum in Newborn MRI Scans. Alcohol Clin Exp Res. 2017 May; 41(5):965-975. PMID: 28247416; PMCID: PMC5404976.
    Citations: 25     Fields:    Translation:Humans
  20. Ou Y, Zöllei L, Retzepi K, Castro V, Bates SV, Pieper S, Andriole KP, Murphy SN, Gollub RL, Grant PE. Using clinically acquired MRI to construct age-specific ADC atlases: Quantifying spatiotemporal ADC changes from birth to 6-year old. Hum Brain Mapp. 2017 06; 38(6):3052-3068. PMID: 28371107.
    Citations: 18     Fields:    Translation:Humans
  21. Ding SL, Royall JJ, Sunkin SM, Ng L, Facer BA, Lesnar P, Guillozet-Bongaarts A, McMurray B, Szafer A, Dolbeare TA, Stevens A, Tirrell L, Benner T, Caldejon S, Dalley RA, Dee N, Lau C, Nyhus J, Reding M, Riley ZL, Sandman D, Shen E, van der Kouwe A, Varjabedian A, Write M, Zollei L, Dang C, Knowles JA, Koch C, Phillips JW, Sestan N, Wohnoutka P, Zielke HR, Hohmann JG, Jones AR, Bernard A, Hawrylycz MJ, Hof PR, Fischl B, LeinReference ES. Comprehensive cellular-resolution atlas of the adult human brain. J Comp Neurol. 2017 02 01; 525(2):407. PMID: 27917481; PMCID: PMC6886049.
    Citations: 14     Fields:    
  22. Ding SL, Royall JJ, Sunkin SM, Ng L, Facer BA, Lesnar P, Guillozet-Bongaarts A, McMurray B, Szafer A, Dolbeare TA, Stevens A, Tirrell L, Benner T, Caldejon S, Dalley RA, Dee N, Lau C, Nyhus J, Reding M, Riley ZL, Sandman D, Shen E, van der Kouwe A, Varjabedian A, Wright M, Zöllei L, Dang C, Knowles JA, Koch C, Phillips JW, Sestan N, Wohnoutka P, Zielke HR, Hohmann JG, Jones AR, Bernard A, Hawrylycz MJ, Hof PR, Fischl B, Lein ES. Comprehensive cellular-resolution atlas of the adult human brain. J Comp Neurol. 2016 11 01; 524(16):3127-481. PMID: 27418273; PMCID: PMC5054943.
    Citations: 95     Fields:    Translation:Humans
  23. Narayanan PL, Warton C, Rosella Boonzaier N, Molteno CD, Joseph J, Jacobson JL, Jacobson SW, Zöllei L, Meintjes EM. Improved segmentation of cerebellar structures in children. J Neurosci Methods. 2016 Mar 15; 262:1-13. PMID: 26743973; PMCID: PMC4970456.
    Citations: 3     Fields:    Translation:Humans
  24. Ou Y, Gollub RL, Retzepi K, Reynolds N, Pienaar R, Pieper S, Murphy SN, Grant PE, Zöllei L. Brain extraction in pediatric ADC maps, toward characterizing neuro-development in multi-platform and multi-institution clinical images. Neuroimage. 2015 Nov 15; 122:246-61. PMID: 26260429; PMCID: PMC4966541.
    Citations: 9     Fields:    Translation:HumansCells
  25. de Macedo Rodrigues K, Ben-Avi E, Sliva DD, Choe MS, Drottar M, Wang R, Fischl B, Grant PE, Zöllei L. A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0-2 year age range. Front Hum Neurosci. 2015; 9:21. PMID: 25741260; PMCID: PMC4332305.
    Citations: 31     
  26. Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, Caldejon S, Carey A, Cuhaciyan C, Dalley RA, Dee N, Dolbeare TA, Facer BA, Feng D, Fliss TP, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Howard RE, Jochim JM, Kuan CL, Lau C, Lee CK, Lee F, Lemon TA, Lesnar P, McMurray B, Mastan N, Mosqueda N, Naluai-Cecchini T, Ngo NK, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry SE, Stevens A, Pletikos M, Reding M, Roll K, Sandman D, Sarreal M, Shapouri S, Shapovalova NV, Shen EH, Sjoquist N, Slaughterbeck CR, Smith M, Sodt AJ, Williams D, Zöllei L, Fischl B, Gerstein MB, Geschwind DH, Glass IA, Hawrylycz MJ, Hevner RF, Huang H, Jones AR, Knowles JA, Levitt P, Phillips JW, Sestan N, Wohnoutka P, Dang C, Bernard A, Hohmann JG, Lein ES. Transcriptional landscape of the prenatal human brain. Nature. 2014 Apr 10; 508(7495):199-206. PMID: 24695229.
    Citations: 534     Fields:    Translation:HumansAnimalsCells
  27. Kolasinski J, Takahashi E, Stevens AA, Benner T, Fischl B, Zöllei L, Grant PE. Radial and tangential neuronal migration pathways in the human fetal brain: anatomically distinct patterns of diffusion MRI coherence. Neuroimage. 2013 Oct 01; 79:412-22. PMID: 23672769.
    Citations: 30     Fields:    Translation:HumansCells
  28. Toews M, Zöllei L, Wells WM. Feature-based alignment of volumetric multi-modal images. Inf Process Med Imaging. 2013; 23:25-36. PMID: 24683955.
    Citations: 9     Fields:    Translation:Humans
  29. Toews M, Wells WM, Zöllei L. A feature-based developmental model of the infant brain in structural MRI. Med Image Comput Comput Assist Interv. 2012; 15(Pt 2):204-11. PMID: 23286050.
    Citations: 11     Fields:    Translation:Humans
  30. Yendiki A, Panneck P, Srinivasan P, Stevens A, Zöllei L, Augustinack J, Wang R, Salat D, Ehrlich S, Behrens T, Jbabdi S, Gollub R, Fischl B. Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy. Front Neuroinform. 2011; 5:23. PMID: 22016733.
    Citations: 237     
  31. Yeo BT, Krienen FM, Sepulcre J, Sabuncu MR, Lashkari D, Hollinshead M, Roffman JL, Smoller JW, Zöllei L, Polimeni JR, Fischl B, Liu H, Buckner RL. The organization of the human cerebral cortex estimated by intrinsic functional connectivity. J Neurophysiol. 2011 Sep; 106(3):1125-65. PMID: 21653723.
    Citations: 2375     Fields:    Translation:Humans
  32. Petrovic A, Zöllei L. Evaluating volumetric brain registration performance using structural connectivity information. Med Image Comput Comput Assist Interv. 2011; 14(Pt 2):524-31. PMID: 21995069.
    Citations: 1     Fields:    Translation:Humans
  33. Augustinack JC, Helmer K, Huber KE, Kakunoori S, Zöllei L, Fischl B. Direct visualization of the perforant pathway in the human brain with ex vivo diffusion tensor imaging. Front Hum Neurosci. 2010; 4:42. PMID: 20577631.
    Citations: 43     
  34. Propper RE, O'Donnell LJ, Whalen S, Tie Y, Norton IH, Suarez RO, Zollei L, Radmanesh A, Golby AJ. A combined fMRI and DTI examination of functional language lateralization and arcuate fasciculus structure: Effects of degree versus direction of hand preference. Brain Cogn. 2010 Jul; 73(2):85-92. PMID: 20378231.
    Citations: 40     Fields:    Translation:Humans
  35. Zöllei L, Stevens A, Huber K, Kakunoori S, Fischl B. Improved tractography alignment using combined volumetric and surface registration. Neuroimage. 2010 May 15; 51(1):206-13. PMID: 20153833.
    Citations: 35     Fields:    Translation:HumansCells
  36. Tu P, Buckner RL, Zollei L, Dyckman KA, Goff DC, Manoach DS. Reduced functional connectivity in a right-hemisphere network for volitional ocular motor control in schizophrenia. Brain. 2010 Feb; 133(Pt 2):625-37. PMID: 20159769; PMCID: PMC2858012.
    Citations: 23     Fields:    Translation:Humans
  37. Postelnicu G, Zollei L, Fischl B. Combined volumetric and surface registration. IEEE Trans Med Imaging. 2009 Apr; 28(4):508-22. PMID: 19273000.
    Citations: 60     Fields:    Translation:Humans
  38. Maddah M, Zöllei L, Grimson WE, Wells WM. Modeling of Anatomical Information in Clustering of White Matter Fiber Trajectories Using Dirichlet Distribution. Proc Workshop Math Methods Biomed Image Analysis. 2008 Jul 15; 2008:1-7. PMID: 21625356.
    Citations: 9     
  39. Maddah M, Zöllei L, Grimson WE, Westin CF, Wells WM. A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI Analysis. Proc IEEE Int Symp Biomed Imaging. 2008; 4543943:105-108. PMID: 19212449.
    Citations: 9     
  40. Mewes AU, Zöllei L, Hüppi PS, Als H, McAnulty GB, Inder TE, Wells WM, Warfield SK. Displacement of brain regions in preterm infants with non-synostotic dolichocephaly investigated by MRI. Neuroimage. 2007 Jul 15; 36(4):1074-85. PMID: 17513129.
    Citations: 10     Fields:    Translation:Humans
  41. Zöllei L, Jenkinson M, Timoner S, Wells W. A marginalized MAP approach and EM optimization for pair-wise registration. Inf Process Med Imaging. 2007; 20:662-74. PMID: 17633738.
    Citations: 7     Fields:    Translation:Humans
  42. Postelnicu G, Zollei L, Desikan R, Fischl B. Geometry driven volumetric registration. Inf Process Med Imaging. 2007; 20:675-86. PMID: 17633739.
    Citations: 2     Fields:    Translation:Humans
  43. Zöllei L, Fisher JW, Wells WM. A unified statistical and information theoretic framework for multi-modal image registration. Inf Process Med Imaging. 2003 Jul; 18:366-77. PMID: 15344472.
    Citations: 6     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.