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Related publications

Data acquisition and pipelines
  • Iglesias JE, Crampsie S, Strand C, Tachrount M, Thomas DL, Holton JL: "Effect of Fluorinert on the Histological Properties of Formalin-Fixed Human Brain Tissue", Journal of Neuropathology & Experimental Neurology, accepted for publication [link to open access article]
  • Mancini M, Crampsie S, Thomas SL, Jaunmuktane Z, Holton JL, Iglesias JE: "A computational pipeline for MRI-informed 3D histology of the human brain", Organization for Human Brain Mapping (OHBM), 2019.
  • Crampsie S, Strand C, Tachrount M, Thomas D, Ourselin S, Iglesias JE, Holton J: "The effect of immersion in Fluorinert on the histological properties of fixed human brain tissue", 119th Meeting of the British Neuropathological Society, 2018.

Atlases:
  • Iglesias JE, Insausti R, Lerma-Usabiaga G, Bocchetta M, Van Leemput K, Greve DN, van der Kouwe A, Fischl B, Caballero-Gaudes C, Paz-Alonso P, "A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology", NeuroImage, 183, December 2018, 314-326. [link to open access article].
  • Saygin ZM & Kliemann D (joint 1st authors), Iglesias JE, van der Kouwe AJW, Boyd E, Reuter M, Stevens A, Van Leemput K, McKee A, Frosch MP, Fischl B, Augustinack JC: "High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas", NeuroImage, 155, July 2017, 370-382. [pdf] [code]
  • Iglesias JE, Insausti R, Lerma-Usabiaga G, Artacho-Figueroa G, Van Leemput K, Ourselin S, Fischl B, Caballero-Gaudes C, Paz-Alonso PM: "A probabilistic atlas of the human thalamus based on ex vivo MRI and histology", Society for Neuroscience (SfN), 2017.
  • Iglesias JE, Insausti R, Caballero-Gaudes C, Lerma-Usabiaga G, Van Leemput K, Ourselin S, Fischl B, Paz-Alonso PM: "A probabilistic atlas of the thalamic nuclei combining ex vivo MRI and histology", Organization for Human Brain Mapping (OHBM), 2017.

Image analysis methods
  • Mancini M, Huo Y, Landman B, Iglesias JE: “Segmentation-aware adversarial synthesis for registration of histology to MRI”,  International Society for Magnetic Resonance in Medicine (ISMRM), 2019.
  • Iglesias JE, Van Leemput K, Golland P, Yendiki A: "Joint inference on structural and diffusion MRI for sequence-adaptive Bayesian segmentation of thalamic nuclei with probabilistic atlases", IPMI 2019, accepted. [pdf]
  • Mancini M, Crampsie S, Thomas DL, Jaunmuktane Z, Holton JL, Iglesias JE: "Hierarchical joint registration of tissue blocks with soft shape constraints for large-scale histology of the human brain", IEEE ISBI, 2019, accepted.
  • Iglesias JE, Modat M, Peter L, Stevens A, Annunziata R, Vercauteren T, Lein E, Fischl B, Ourselin S, for the ADNI: "Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections", Medical Image Analysis, 50, December 2018, Pages 127-144.  [link to open access article]    [pdf of preprint]
  • Iglesias JE, Lorenzi M, Ferraris S, Peter L, Modat M, Stevens A, Fischl B, Vercauteren T: "Model-based refinement of nonlinear registrations in 3D histology reconstruction", MICCAI 2018, vol 2, 147-155. [pdf] 
  • Atzeni A, Jansen M, Ourselin S, Iglesias JE: "A probabilistic model combining deep learning and multi-atlas segmentation for semi-automated labelling of histology", MICCAI 2018, vol 2, 219-227. [pdf]
  • Iglesias JE, Lerma-Usabiaga G, Garcia-Peraza-Herrera L, Martinez S, Paz-Alonso PM: "Retrospective head motion estimation in structural brain MRI with 3D CNNs", MICCAI 2017, vol 2, 314-322. [pdf]
  • Pichat J, Iglesias JE, Nousias S, Yousry T, Ourselin S, Modat M: "Part-to-whole Registration of Histology and MRI using Shape Elements", ICCV Bioimage Computing Workshop, 107-115. [pdf]
  • Iglesias JE: "Globally optimal coupled surfaces for semi-automatic segmentation of medical images". Proceedings of IPMI 2017, 610-621. [pdf]

Surveys, correspondences, etc.:
  • Stewart W, Allinson K, Al-Sarraj S, Bachmeier C, Barlow K, Belli A, Burns MP, Carson A, Crawford F, Dams-O'Connor K, Diaz-Arrastia R, Dixon CE, Edlow BL, Ferguson S, Fischl B, Folkerth RD, Gentleman S, Giza CC, Grady MS, Helmy A, Herceg M, Holton JL, Howell D, Hutchinson PJ, Iacono D, Iglesias JE, Ikonomovic MD, Johnson VE, Keene CD, Kofler JK, Koliatsos VE, Lee EB, Levin H, Lifshitz J, Ling H, Loane DJ, Love S, Maas AIR, Marklund N, Master CL, McElvenny DM, Meaney DF, Menon DK, Montine TJ, Mouzon B, Mufson EJ, Ojo JO, Prins M, Revesz T, Ritchie CW, Smith C, Sylvester R, Tang CY, Trojanowski JQ, Urankar K, Vink R: "Primum non nocere: a call for balance when reporting on CTE", The Lancet Neurology, 18(3), 2019, 231-233. [read online]
  • Pichat J, Iglesias JE, Yousry T, Ourselin S, Modat M: “A Survey of Methods for 3D Histology Reconstruction”. Medical Image Analysis, 46, May 2018, 73-105. [pdf]

Applications:
  • Bocchetta M, Iglesias JE, Cash DM, Warren JD, Rohrer JD: "Amygdalar subnuclei are differentially affected in the different genetic and pathological forms of frontotemporal dementia", Alzheimers & Dementia: Diagnosis, Assessment & Disease Monitoring, accepted for publication.
  • Chen LW, Sun D, Davis SL, Haswell CC, Dennis EL, Swanson CA, Whelan CD, Gutman B, Jahanshad N, Iglesias JE, Thompson P, Wagner HR, Saemann P, Labar KS, Morey RA, "Smaller hippocampal CA1 subfield volume in posttraumatic stress disorder", Depression and Anxiety, in press.
  • Bocchetta M, Iglesias JE, Scelsi MA, Cash DM, Cardoso MJ, Modat M, Altmann A, Ourselin S, Warren JD, Rohrer JD: "Hippocampal subfield volumetry: differential pattern of atrophy in different forms of genetic frontotemporal dementia", Journal of Alzheimer's Disease, 64 (2), June 2018, 497-504. [link to open access article]
  • Scelsi M, Iglesias JE, Schott JM, Ourselin S, Altman A: "Rare genetic events in sporadic Alzheimer’s disease: a network propagation approach", Organization for Human Brain Mapping (OHBM), 2018.
  • Scelsi M, Iglesias JE, Schott J, Ourselin S, Altmann A: "The role of hippocampal subfields in the atrophy process in Alzheimer's Disease: an in-vivo study of the ADNI cohort ", Alzheimer's Association International Conference (AAIC), 2017.

Other related work:
  • Walsh P, Thomas DL, Sudre CH, Iglesias JE, Crampsie S, Jaunmuktane Z, Holton JL, Ruan NS, Barnes J, Lashley T: "White matter hyperintensities and pathological correlations in Alzheimer's disease", 120th Meeting of the British Neuropathological Society, 2019.
  • Ferraris S, van der Merle J, Van Der Veeken L, Prados F, Iglesias JE, Melbourne A, Lorenzi M, modet M, Gsell W, Deprest J, Vercauteren T: "A magnetic resonance multi-atlas for the neonatal rabbit brain", NeuroImage, 179, October 2018, 187-198.
  • Tella-Amo M, Peter L, Shakir DI, Deprest J, Stoyanov D, Iglesias JE, Vercauteren T, Ourselin S: “Probabilistic visual and electromagnetic data fusion for robust drift-free sequential mosaicking. Application to fetoscopy”, Journal of Medical Imaging, 021217, 2018. [pdf]
  • Arganda-Carreras I, Manoliu T, Mazuras N, Schulze F, Iglesias JE, Bühler K, Jenett A, Rouyer F, Andrey P: "A statistically representative atlas for mapping neuronal circuits in the Drosophila adult brain", Frontiers in Neuroinformatics, 12, 2018, 13. [link to open access article]
  • Morrell S, Wojna Z, Koo CS, Ourselin S, Iglesias JE: "Large-scale mammography CAD with Deformable Conv-Nets", MICCAI 2018 Workshop in Breast Image Analysis, 64-72.
  • Iglesias JE, Ferraris S, Modat M, Gsell W, Deprest J, van der Merwe JL, Vercauteren T: "Template-free estimation of intracranial volume: a preterm birth animal model study", Fetal and Infant Image Analysis, 2017, 3-13. [pdf]
  • Aganj I, Iglesias JE, Reuter M, Sabuncu M, Fischl B: "Mid-Space-Independent Deformable Image Registration", NeuroImage, 152, May 2017, 158-170. [pdf]
  • Zöllei L, Ou Y, Iglesias JE, Grant PE, Fischl B: "FreeSurfer image processing pipeline for infant clinical MRI images", Organization for Human Brain Mapping (OHBM), 2017.

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