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Related publications

Data acquisition and pipelines
  • Mancini M, Casamitjana A, Peter L, Robinson E, Crampsie S, Thomas DL, Holton JL, Jaunmuktane Z, Iglesias JE: "A multimodal computational pipeline for 3D histology of the human brain", Scientific Reports, accepted for publication. [link to preprint]  [video1]  [video2]
  • 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, 77 (12), 2018, 1085-1090 [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
  • Billot B, Robinson E, Dalca A, Iglesias JE: “Partial Volume Segmentation of Brain MRI Scans of any Resolution and Contrast”, Proceedings of MICCAI 2020 (accepted). [arxiv]
  • Yu E, Dalca AV, Iglesias JE, Sabuncu MR: "An Auto-Encoder Strategy for Adaptive Image Segmentation", Proceedings of MIDL 2020 (accepted). [arxiv].
  • Billot B, Greve DN, Van Leemput K, Fischl B, Iglesias JE*, Dalca AV*: "A learning strategy for contrast-agnostic MRI segmentation", Proceedings of MIDL 2020 (accepted). [arxiv] (* joint senior authors)
  • Dalca AV, Yu E, Golland P, Fischl B, Sabuncu M, Iglesias JE: “Unsupervised deep learning for Bayesian brain MRI segmentation”, Proceedings of MICCAI 2019, 356-365. [link to ArXiv paper]
  • 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, accepted for publication. [arxiv]
  • 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, Neason M, Cash DM, Warren JD, Rohrer JD: "Thalamic nuclei in frontotemporal dementia: mediodorsal nucleus involvement is universal but pulvinar atrophy is unique to C9orf72", Human Brain Mapping, accepted for publication.
  • Bocchetta M, Iglesias JE, Chelban V, Jabbari E, Lamb R, Russell LL, Greaves CV, Neason M, Cash DM, Thomas DL, Warren JD, Woodside J, Morris HR, Rohrer JD: "Automated brainstem segmentation detects differential involvement in atypical parkinsonian syndromes", Journal of Movement Disorders, in press.
  • Bocchetta M, Iglesias JE, Russell LL, Greaves CV, Marshall CR, Scelsi MA, Cash DM, Ourselin S, Warren JD, Rohrer JD: "Segmentation of medial temporal subregions reveals early right-sided involvement in semantic variant PPA", Alzheimer's Research & Therapy, 11 (1), May 2019, 41-50.
  • 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:
  • Aganj I, Frau-Pascual A, Iglesias JE, Yendiki A, Augustinack J, Salat D, Fischl B: "Compensatory Brain Connection Discovery in Alzheimer’s Disease", Proceedings of IEEE ISBI 2020 (accepted).
  • Tregidgo H, Casamitjana A, Latimer C, Kilgore M, Robinson E, Blackburn E, Van Leemput K, Fischl B, Dalca A, MacDonalds C, Keene CD, Iglesias JE: "3D reconstruction and segmentation of dissection photographs for MRI-free neuropathology", Proceedings of MICCAI 2020 (accepted).
  • Brown EM, Pierce ME, Clark DC, Fischl B, Iglesias JE, McGlinchey RE, Milberg WP, Salat DH: "Test-Retest Reliability of FreeSurfer Automated Hippocampal Subfield Segmentation Within and Across Scanners", Neuroimage, accepted for publication.
  • 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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