Journal papers
  • 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, accepted for publication. [pdf]
  • Aganj I, Iglesias JE, Reuter M, Sabuncu M, Fischl B: "Mid-Space-Independent Deformable Image Registration", NeuroImage, 152, May 2017, 158-170. [pdf]
  • Ho NF, Holt DJ, Cheung M, Iglesias JE, Goh A, Wang M, Lim JKW, de Souza J, Poh JS, See YM, Adcock AR, Wood SJ, Chee MWL, Lee J, Zhou J: "Progressive Decline in Hippocampal CA1 Volume in Individuals at Ultra-High-Risk for Psychosis Who Do Not Remit: Findings from the Longitudinal Youth at Risk Study", Neuropsychopharmacology, accepted for publication.
  • Puonti O, Iglesias JE, Van Leemput K: "Fast and Sequence-Adaptive Whole-Brain Segmentation Using Parametric Bayesian Modeling", Neuroimage, 143, December 2016, 245-249. [pdf]
  • Iglesias JE, Van Leemput K, Augustinack J, Insausti R, Fischl B, Reuter M: "Bayesian longitudinal segmentation of hippocampal substructures in brain MRI using subject-specific atlases", Neuroimage, 141, November 2016, 542-555. [ScienceDirect (open access article)]  or  [pdf of preprint]
  • Lerma-Usabiaga G, Iglesias JE, Insausti R, Greve DN, Paz-Alonso PM: "Automated Segmentation of the Human Hippocampus Along Its Longitudinal Axis", Human Brain Mapping, 37(9), September 2016, 3353-3367.
  • Cantero JL, Iglesias JE, Van Leemput K, Atienza M: "Regional Hippocampal Atrophy and Higher Levels of Plasma Amyloid-Beta are Associated with Subjective Memory Complaints in Nondemented Elderly Subjects". The journals of gerontology. Series A, Biological sciences and medical sciences, in press. [Link to paper, hosted in JL Cantero's lab website]
  • Whelan CD, Hibar DP, van Velzen LS, Zannas AS, Carrillo-Roa T, McMahon K, Prasad G, Kelly S, Faskowitz J, de Zubicaray G, Iglesias JE, van Erp TGM, Frodl T, Martin NG, Wright MJ, Jahanshad N, Schmaal L, Sämann PG, Thompson PM, for the ADNI: "Heritability and reliability of automatically segmented human hippocampal formation subregions", Neuroimage, 128, March 2016, 125-137. [ScienceDirect (open access article)]
  • Ho NF, Iglesias JE, Sum MY, Kuswanto C, Sitoh YY, Souza J, Hong Z, Fischl B, Roffman J, Zhou J, Sim K, Holt D: "Progression from selective to general involvement of hippocampal subfields in schizophrenia". Molecular Psychiatry, 22, 2016, 142-152.  [, open access].
  • Sacchet M, Livermore EE, Iglesias JE, Glover GH, Gotlib IH: "Subcortical Volumes Differentiate Major Depressive Disorder, Bipolar Disorder, and Remitted Major Depressive Disorder". Journal of Psychiatric Research, 68, September 2015, 91-98.
  • Iglesias JE, Sabuncu MR: "Multi-Atlas Segmentation of Biomedical Images: A Survey", Medical Image Analysis, 24(1), August 2015, 205–219. [pdf]  (we also have a preprint at
  • Iglesias JE, Augustinack JC, Nguyen K, Player CM, Player A, Wright M, Roy N, Frosch MP, McKee AC, Wald LL, Fischl B, Van Leemput K, for the ADNI: "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI", Neuroimage, 115, July 2015, 117-137[ScienceDirect (open access article)]    [code]
  • Iglesias JE, Van Leemput K, Bhatt P, Casillas C, Dutt S, Schuff N, Truran-Sacrey D, Boxer A, Fischl B, for the ADNI: "Bayesian segmentation of brainstem structures in MRI", NeuroImage, 113, June 2015, 184-195. [ScienceDirect (open access article)]     [code]
  •  Yushkevich PA, Amaral RSC, Augustinack JC, Bender AR, Bernstein JD, Boccardi M, Bocchetta M, Burggren AC, Carr VA, Chakravarty MM, Chetelat G, Daugherty AM, Davachi L, Ding S, Ekstrom A, Geerlings MI, Hassan A, Huang Y, Iglesias JE, La Joie R, Kerchner GA, LaRocque KF, Libby LA, Malykhin N, Mueller SG, Olsen RK, Palombo DJ, Parekh MB, Pluta JB, Preston AR, Pruessner JC, Ranganath C, Raz N, Schlichting ML, Schoemaker D, Singh S, Stark CEL, Suthana N, Tompary A, Turowski MM, Van Leemput K, Wagner AD, Wang L, Winterburn JL, Wisse LEM, Yassa MA, Zeineh MM, for the Hippocampal Subfields Group (HSG): "Quantitative comparison of 21 protocols for labeling hippocampal subfields and parahippocampal subregions in in vivo MRI: Towards a harmonized segmentation protocol", NeuroImage, 111, May 2015, 526-541.
  • Iglesias JE, Sabuncu MR, Aganj I, Bhatt P, Casillas C, Salat D, Boxer A, Fischl B, Van Leemput K: "An algorithm for optimal fusion of atlases with different labeling protocols", NeuroImage, 106,2015, 451-463. [ScienceDirect (open access article)]
  • Iglesias JE, Sabuncu MR, Van Leemput K: "A Unified Framework for Cross-modality Multi-atlas Segmentation of Brain MRI", Medical Image Analysis, 17(8), 2013, 1181-1191.
  • Liu CY, Iglesias JE, Tu Z: "Deformable Templates Guided Discriminative Models for Robust 3D Brain MRI Segmentation", Neuroinformatics, 11(4), 2013, 447-468.
  • Iglesias JE, Sabuncu MR, Van Leemput K: "Improved Inference in Bayesian Segmentation Using Monte Carlo Sampling: Application to Hippocampal Subfield Volumetry", Medical Image Analysis (special issue MICCAI 2012), 17(7),2013, 766-778. [pdf]
  • Iglesias JE, Liu CY, Thompson P, Tu Z: "Robust Brain Extraction Across Datasets and Comparison with Publicly Available Methods", IEEE Transactions on Medical Imaging, 30(9), 2011, 1617-1634. [pdf]   [code]
  • Iglesias JE, Thompson P, Zhao A, Tu Z: "Modeling diffusion-weighted MRI as a spatially-variant Gaussian mixture: application to image denoising", Medical Physics, 38(7), 2011, 4350-4364.
  • Iglesias JE, Thompson P, Liu CY, Tu Z: "Fast Approximate Stochastic Tractography", Neuroinformatics, 10(1), 2012, 5-17.
  • Iglesias JE, Karssemeijer N: "Robust Initial Detection of Landmarks in Film-Screen Mammograms Using Multiple FFDM Atlases", IEEE Transactions on Medical Imaging, 28(11), pp. 1815-1824, November 2009.
  • Iglesias JE, de Bruijne M: "Semi-automatic segmentation of vertebrae in lateral X-rays using a conditional shape model", Academic Radiology, 14(10), 2007, 1156-1165.
  • Del Rio G, Iglesias JE, Martinez J: "A comparison of floorplan design strategies in Architecture and Engineering", Automation in Construction, 16(5), August 2007, 559-568.
  • Del Rio G, Martinez J, Iglesias JE: "A multidisciplinary model for floorplan design", International Journal of Production Research, 45(15), August 2007, 3457-3476.
Conference papers
  • 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, accepted. [pdf]
  • Iglesias JE: "Globally optimal coupled surfaces for semi-automatic segmentation of medical images". Proceedings of IPMI 2017 (accepted).
  • Glocker B, Konukoglu E, Lavdas I, Iglesias JE, Aboagye EO, Rockall AG, Rueckert D: "Correction of Fat-Water Swaps in Dixon MRI", MICCAI 2016, vol 3, 536-543. [pdf] 
  • Iglesias JE, Paz-Alonso PM, Lerma-Usabiaga G, Insausti R, Miller K, Caballero-Gaudes C: "Simultaneous Bayesian correction of slab boundary artifacts and bias field for high resolution ex vivo MRI", Proceedings of IEEE ISBI 2016, 1384-1387. [pdf]    [code] 
  • Aganj I, Iglesias JE, Reuter M, Sabuncu MR, Fischl B: “Mid-space-independent symmetric data term for pairwise deformable image registration”, MICCAI 2015, vol 2, 263-271. [pdf]
  • Iglesias JE, Sabuncu MR, Van Leemput K: "A Probabilistic, Non-parametric Framework for Inter-modality Label Fusion", Proceedings of MICCAI 2013, vol 3, 576-583. [pdf]
  • Iglesias JE, Konukoglu E, Zikic D, Glocker B, Van Leemput K, Fischl B: "Is Synthesizing MRI Contrast Useful for Inter-Modality Analysis?", Proceedings of MICCAI 2013, vol 1,  631-638. [pdf]
  • Puonti O, Iglesias JE, Van Leemput K: "Fast, Sequence Adaptive Parcellation of Brain MR Using Parametric Models", Proceedings of MICCAI 2013, vol 1, 727-734..
  • Iglesias JE, Sabuncu MR, Van Leemput K: "Incorporating Parameter Uncertainty in Bayesian Segmentation Models: Application to Hippocampal Subfield Volumetry", Proceedings of MICCAI 2012, vol 3, 50-57. [pdf]
  • Iglesias JE, Sabuncu MR, Van Leemput K: "A Generative Model for Multi-atlas Segmentation across Modalities", Proceedings of IEEE ISBI 2012, 888-891. [pdf]
  • Iglesias JE, Jiang J, Liu CY, Tu Z, ADNI: "Classification of Alzheimer's Disease Using a Self-Smoothing Operator", Proceedings of MICCAI 2011, vol 3, 58-65.
  • Speier W, Iglesias JE, El-Kara L, Tu Z, Arnold CW: "Robust Skull Stripping of Clinical Glioblastoma Multiforme Data", Proceedings of MICCAI 2011, vol 3, 659-666.
  • Iglesias JE, Konukoglu E, Montillo A, Tu Z, Criminisi A: "Combining Generative and Discriminative Models for Semantic Segmentation of CT Scans via Active Learning", Proceedings of IPMI 2011, 25-36.
  • Montillo A, Shotton J, Winn J, Iglesias JE, Metaxas D, Criminisi A: "Entangled Decision Forests and their Application for Semantic Segmentation of CT Images", Proceedings of IPMI 2011, 184-196.
  • Iglesias JE, Thompson P, Liu CY, Tu Z: "Agreement-based Semi-Supervised Learning for Skull Stripping", Proceedings of MICCAI 2010, pp. 81-88.
  • Iglesias JE, Dinov I, J Singh, GE Tong, Tu Z: "Synthetic MRI signal standardization: application to multi-atlas hippocampus segmentation", proceedings of MICCAI 2010, pp. 147-154.
  • Iglesias JE, Thompson P, Liu CY, Tu Z: "Discretizing stochastic tractography: a fast implementation", Proceedings of IEEE ISBI 2010, pp. 1381-1384.
  • Liu CY, Toga A, Iglesias JE, Tu Z: "Fusing adaptive atlas and informative features for robust 3D brain image segmentation", Proceedings of IEEE ISBI 2010, pp 848-851.
  • Iglesias JE, Rocks K, Jahanshad N, Frias-Martinez E, Andrada L, Bui A: "Tracking medication information across medical records", Proceedings of AMIA 2009, pp. 266-270.
  • Iglesias JE, de Bruijne M, Loog M, Lauze F, Nielsen M: "A family of principal component analyses for dealing with outliers", Proceedings of MICCAI 2007, pp. 178-185.

Book Chapters
  • Montillo A, Tu J, Shotton J, Winn J, Iglesias JE, Metaxas DN, Criminisi A: "Entanglement and Differentiable Information Gain Maximization", in: Criminisi A, Shotton J: "Decision Forests for Computer Vision and Medical Image Analysis", Springer, 2013.
  • Taira RK, Iglesias JE, Jahanshad N: "Characterizing Image Data", in: Bui ATT, Taira RK: "Medical Imaging Informatics", Springer, 2009.

  • "Semi-automatic contour detection". Applicants: Nordic Bioscience Imaging A/S, de Bruijne M, Iglesias JE. Patent publication number: WO/2008/141996. Publication date: 27 Nov. 2008.

Papers in conference workshops
  • Larsen CT, Iglesias JE, Van Leemput K: "N3 Bias Field Correction Explained as a Bayesian Modeling Method", Bayesian and Graphical Models for Biomedical Imaging 2013, pp. 1-12. [pdf] 
  • Iglesias JE, Sabuncu MR, Van Leemput K: "Probabilistic label fusion with a parametric generative model", Proceedings of MICCAI Workshop on Segmentation: Algorithms, Theory and Applications 2013, pp. 128-131. [pdf]
  • Iglesias JE, Sabuncu MR, Van Leemput K: "A Generative Model for Probabilistic Label Fusion of Multimodal Data", Multimodal Brain Image Analysis 2012, pp. 115-133. [pdf]
  • Liu CY, Iglesias JE, Toga A, Tu Z: "Pictorial multi-atlas segmentation of brain MRI", Mathematical Methods in Biomedical Image Analysis 2012, pp. 65-70.
  • Iglesias JE, Thompson P, Tu Z: "A spatially variant mixture model for diffusion weighted MRI: application to image denoising", Probabilistic Models For Medical Image Analysis, workshop at MICCAI 2009, pp. 103-114.

Conference presentations
  • 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.
  • 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.
  • 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.
  • Krishnaswamy P, Obregon-Henao G, Ahveninen J,Khan S, Babadi B, Iglesias JE, Hamalainen M, Pardon P, "Hierarchical Sparsity-Based Estimation Approach Resolves Subcortical Sources Underlying M/EEG Data", Organization for Human Brain Mapping (OHBM), 2016.
  • Lerma-Usabiaga G, Iglesias JE, Insausti R, Greve D, Paz-Alonso PM: "Automated Segmentation of the Human Hippocampus Longitudinal Axis", Organization for Human Brain Mapping (OHBM), 2016.
  • Iglesias JE, Paz-Alonso PM, Lerma-Usabiaga G, Insausti R, Miller K, Caballero-Gaudes C: “Bayesian correction of bias field and Venetian blind for high resolution ex vivo MRI with clinical scanners”,  International Society for Magnetic Resonance in Medicine (ISMRM), 2015.   [code] 
  • Ho NF, Iglesias JE, Sum MY, Fischl B, Zhou J, Sim K: "Longitudinal study of hippocampal subfield volumes in schizophrenia and bipolar disorder", International Congress of Schizophrenia Research, 2015. Abstract can be found in Schizophrenia Bulletin, vol. 41, pp. S257-258.
  • Lerma-Usabiaga G, Iglesias JE, Paz-Alonso PM: "Hippocampal longitudinal axis segmentation: PCA-based automated segmentation tool", Society for Neuroscience, 2015.
  • Lerma-Usabiaga G, Iglesias JE, Paz-Alonso PM: "PCA-based automatic segmentation of hippocampal longitudinal axis", Cognitive Neuroscience Society, 2015.
  • Sacchet MD, Livermore E, Iglesias JE, Glover GH, Gotlib IH: “Subcortical Volumes Differentiate Among Affective Disorders”. Organization for Human Brain Mapping, 2015.
  • Sacchet MD, Livermore E, Iglesias JE, Glover GH, Gotlib IH: “Subcortical Volumes Differentiate Affective Disorders”. Society for Biological Psychiatry, 2015.
  • Arganda-Carreras I, Iglesias JE, Jenett A, Manoliu T, Rouyer F, Andrey P: “Group-wise registration methods to construct statistical atlases of Drosophila adult brains”. VIB Conference on Biomage Informatics, 2014.
  • Mueller SG, Yushkevic P, Wang L, van Leemput K, Mezher A, Das S, Iglesias JE, Weiner MW: “Collaboration for a Systematic Comparison of Different Techniques to Measure Subfield Volumes: Announcement and First Results”. Alzheimer's Association International Conference 2013. [pdf]
  • Ho NF, Coombs G, Nitenson A, Iglesias JE, Henderson DC, Roffman JL, Holt DJ: "Intrinsic Functional Connectivity of the Dentate Gyrus of the Hippocampus is Altered in Schizophrenia", oral presentation at the International Congress of Schizophrenia Research 2013.
  • Iglesias JE, Kimiaei S: "Respiratory Motion Correction in PET with gated PET/CT data", poster at ESNM'06 (annual meeting of the European Society of Nuclear Medicine).