Deep-MI Lab
← Deep-MI Lab

Publications

Peer-reviewed publications from Deep-MI: AI in Medical Imaging Lab. When using our tools please cite the relevant papers.

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Rassmann S, Kügler D, Brunheim S, Ehses P , Reuter M. Rethinking Real-World MRI Denoising: Learning from Physical Noise. European Conference on Computer Vision (ECCV). 2026 (to appear).

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Ewert C, Kügler D, Reuter M. Learning-based Segmentation of Diffusion-Weighted MR Images with Arbitrary q-Space Samplings. Imaging Neuroscience. 2026.

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Pollak C, Diers K, Estrada S., Kügler D, Reuter M. FastSurfer-CC: A robust, accurate, and comprehensive framework for corpus callosum morphometry. Imaging Neuroscience. 2026.

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Rassmann S, Kügler D, Ewert C, Reuter M. Regression is all you need for medical image translation. IEEE Transactions on Medical Imaging. 2026.

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Pollak C, Kügler D, Bauer T, Rüber T, Reuter M. FastSurfer-LIT: Lesion inpainting tool for whole-brain MRI segmentation with tumors, cavities, and abnormalities. Imaging Neuroscience. 2025.

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Xu P, Estrada S, Etteldorf R, Liu D, Shahid M, Zeng W, Früh D, Reuter M, Breteler MMB, Aziz NA. Hypothalamic volume is associated with age, sex and cognitive function across lifespan: a comparative analysis of two large population-based cohort studies. eBioMedicine. 2025.

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Koch A, Stirnberg R, Estrada S, Zeng W, Lohner V, Shahid M, Ehses P, Pracht E, Reuter M*, Stöcker T*, Breteler MMB*. (*co-last). Versatile MRI acquisition and processing protocol for population-based neuroimaging. Nature Protocols. 2024.

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Henschel L, Kügler D, Zöllei L*, Reuter M*. (*co-last). VINNA for Neonates – Orientation Independence through Latent Augmentations. Imaging Neuroscience. 2024.

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Ewert C*, Kügler D*, Stirnberg R, Koch A, Yendiki A, Reuter M. (*co-first). Geometric Deep Learning for Diffusion MRI Signal Reconstruction with Continuous Samplings (DISCUS). Imaging Neuroscience. 2024.

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Estrada S, Kügler D, Bahrami E, Xu P, Mousa D, Breteler MMB, Aziz NA, Reuter M. FastSurfer-HypVINN: Automated sub-segmentation of the hypothalamus and adjacent structures on high-resolutional brain MRI. Imaging Neuroscience. 2023.

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Diers K, Baumeister H, Jessen F, Düzel E, Berron D, Reuter M. An automated, geometry-based method for hippocampal shape and thickness analysis. NeuroImage. 2023.

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Pollak C, Kügler D, Breteler MMB, Reuter M. Quantifying MR head motion in the Rhineland Study – A robust method for population cohorts. NeuroImage. 2023.

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Pollak C*, Kügler D*, Reuter M. (*co-first). Estimating Head Motion from MR-Images. IEEE 20th International Symposium on Biomedical Imaging (ISBI). 2023.

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Faber J*, Kügler D*, Bahrami E*, Heinz LS, Timmann D, Ernst TM, Deike-Hofmann K, Klockgether T, van de Warrenburg B, van Gaalen J, Reetz K, Romanzetti S, Oz G, Joers JM, Diedrichsen J, ESMMR Study Group, Reuter M. (*co-first). CerebNet: A fast and reliable deep-learning pipeline for detailed cerebellum sub-segmentation. NeuroImage. 2022.

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Henschel L, Kügler D, Reuter M.. Identifying and Combating Bias in Segmentation Networks by leveraging multiple resolutions. Medical Image Computing and Computer-Assisted Interventions, International Conference of (MICCAI). 2022.

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Saikat R*, Kügler D*, Reuter M. (*co-first). Are 2.5D approaches superior to 3D deep networks in whole brain segmentation?. Medical Imaging with Deep Learning, Conference (MIDL). 2022.

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Henschel L*, Kügler D*, Reuter M. (*co-first). FastSurferVINN: Building Resolution-Independence into Deep Learning Segmentation Methods - A Solution for HighRes Brain MRI. NeuroImage. 2022.

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Mauschitz MM, Lohner V, Koch A, Stöcker T, Reuter M, Holz FG, Finger RP, Breteler MMB. Retinal layer assessments as potential biomarkers for brain atrophy in the Rhineland Study. Scientific Reports. 2022.

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Harms A, Bauer T, Fischbach L, David B, Ernst L, Witt J-A, Diers K, Baumgartner T, Weber B, Radbruch A, Becker AJ, Helmstaedter C, Reuter M, Elger CE, Surges R, Rüber T. Shape description and volumetry of hippocampus and amygdala in temporal lobe epilepsy – A beneficial combination with a clinical perspective. Epilepsy & Behavior. 2022.

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Lu R, Aziz NA, Reuter M, Stöcker T, Breteler MMB. Evaluation of the Neuroanatomical Basis of Olfactory Dysfunction in the General Population. JAMA Otolaryngol Head Neck Surg. 2021.

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Estrada S, Lu R, Diers K, Zeng W, Ehses P, Stöcker T, Breteler MMB, Reuter M. Automated olfactory bulb segmentation on high resolutional T2-Weighted MRI. NeuroImage. 2021.

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Hoffmann M, Turk EA, Gagoski B, Morgan L, Wighton P, Tisdall MD, Reuter M, Adalsteinsson E, Grant PE, Wald LL, van der Kouwe AJW. Rapid head-pose detection for automated slice prescription of fetal-brain MRI. IMA. 2021.

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Lu R, Aziz A, Diers K, Stöcker T, Reuter M, Breteler MMB. Insulin resistance accounts for metabolic syndrome-related alterations in brain structure. Human Brain Mapping. 2021.

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Henschel L, Reuter M. Parameter Space CNN for Cortical Surface Segmentation. Bildverarbeitung für die Medizin 2020. Informatik aktuell. 2020.

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Ewert C, Kügler D, Yendiki A, Reuter M. Learning Anatomical Segmentations for Tractography from Diffusion MRI. MICCAI Workshop on Computational Diffusion MRI. 2020.

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Henschel L, Conjeti S, Estrada S, Diers K, Fischl B, Reuter M. FastSurfer - A fast and accurate deep learning based neuroimaging pipeline. NeuroImage. 2020.

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Estrada S, Lu R, Conjeti S, Orozco‐Ruiz X, Panos‐Willuhn J, Breteler MMB, Reuter M. FatSegNet: A Fully Automated Deep Learning Pipeline for Adipose Tissue Segmentation on Abdominal Dixon MRI. MRM. 2019.

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Estrada S, Conjeti S, Ahmad M, Nassir N, Reuter M. Competition vs. Concatenation in Skip Connections of Fully Convolutional Networks. MICCAI - International Workshop on Machine Learning in Medical Imaging. 2018.

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Ahmad M, Conjeti S, Estrada S, Ehses P, Stöcker T, Reuter M. Complex Fully Convolutional Neural Networks for MR Image Reconstruction. MICCAI - International Workshop on Machine Learning for Medical Image Reconstruction. 2018.

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Zaretskaya N, Fischl B, Reuter M, Renvall V, Polimeni JR. Advantages of cortical surface reconstruction using submillimeter 7T MEMPRAGE. NeuroImage. 2018.

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Schwarz JM, Pracht ED, Brenner D, Reuter M, Stöcker T. GRAPPA reconstructed wave‐CAIPI MP‐RAGE at 7 Tesla. MRM. 2018.

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Wachinger C, Nho K, Saykin AJ, Reuter M, Rieckmann A. A Longitudinal Imaging Genetics Study of Neuroanatomical Asymmetry in Alzheimer’s Disease. Biol Psychiatry. 2018.

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Ranjan C, Paynabar K, Reuter M, Jafari-Khouzani K. Longitudinal MRI Data Analysis in Presence of Measurement Error but Absence of Replicates. IISE Trans Healthc Syst Eng. 2018.

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Wachinger C, Reuter M, Klein T. DeepNAT: Deep convolutional neural network for segmenting neuroanatomy. NeuroImage. 2018.

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Wachinger C, Rieckmann A, Reuter M. Latent Processes Governing Neuroanatomical Change in Aging and Dementia. MICCAI. 2017.

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Berron D, Schütze H, Cardenas-Blanco A, Fliessbach K, Wagner M, Spottke A, Reuter M, Teipel SJ, Buerger K, Schneider A, Peters O, Nestor P, Priller J, Wiltfang J, Laske C, Jessen F, Düzel E. Object and Scene Memory are Differentially Associated with CSF Markers OF Alzheimer’s Disease and MRI Volumetry. Alzheimers Dement. 2017.

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Saygin, ZM, Kliemann D, 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. 2017.

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Klein A, Ghosh SS, Bao FS, Giard J, Häme Y, Stavsky E, Lee N, Rossa B, Reuter M, Chaibub Neto E, Keshavan A. Mindboggling morphometry of human brains. Comput Biol. 2017.

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Aganj I, Iglesias JE, Reuter M, Sabuncu MR, Fischl B. Mid-space-independent deformable image registration. NeuroImage. 2017.

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Wachinger C, Salat DH, Weiner M, Reuter M. Whole-brain analysis reveals increased neuroanatomical asymmetries in dementia for hippocampus and amygdala. Brain. 2016.

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Ge T, Reuter M, Winkler AM, Holmes AJ, Lee PH, Tirrell LS, Roffman JL, Buckner RL, Smoller JW, Sabuncu MR. Multidimensional heritability analysis of neuroanatomical shape. Nat Commun. 2016.

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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. 2016.

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Wachinger C, Reuter M. Domain adaptation for Alzheimer’s disease diagnostics. NeuroImage. 2016.

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Yendiki A, Reuter M, Wilkens P, Rosas HD, Fischl B. Joint reconstruction of white-matter pathways from longitudinal diffusion MRI data with anatomical priors. NeuroImage. 2016.

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Tisdall MD, Reuter M, Qureshi A, Buckner RL, Fischl B, van der Kouwe A. Prospective motion correction with volumetric navigators (vNavs) reduces the bias and variance in brain morphometry induced by subject motion. NeuroImage. 2016.

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Biller A, Reuter M, Patenaude B, Homola GA, Breuer F, Bendszus M, Bartsch AJ. Responses of the Human Brain to Mild Dehydration and Rehydration Explored In Vivo by 1H-MR Imaging and Spectroscopy. Am J Neuroradiol. 2015.

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Aganj I, Iglesias JE, Reuter M, Sabuncu MR, Fischl B. Mid-Space-Independent Symmetric Data Term for Pairwise Deformable Image Registration. MICCAI. 2015.

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Cash DM, Frost C, Iheme LO, Ünay D, Kandemir M, Fripp J, Salvado O, Bourgeat P, Reuter M, Fischl B, Lorenzi M, Frisoni GB, Pennec X, Pierson RK, Gunter JL, ML Senjem, Jack CR, Guizard JN, Fonov VS, Collins DL, Modat M, Cardoso MJ, Leung KK, Wang H, Das SR, Yushkevich PA, Malone IB, Fox NC, Schott JM, Ourselin S. Assessing atrophy measurement techniques in dementia: Results from the MIRIAD atrophy challenge. NeuroImage. 2015.

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Wachinger C, Golland P, Kremen W, Fischl B, Reuter M. BrainPrint: a discriminative characterization of brain morphology. NeuroImage. 2015.

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Bron EE, Smits M, van der Flier WM, Vrenken H, Barkhof F, Scheltens P, Papma JM, Steketee RM, Méndez Orellana C, Meijboom R, Pinto M, Meireles JR, Garrett C, Bastos-Leite AJ, Abdulkadir A, Ronneberger O, Amoroso N, Bellotti R, Cárdenas-Peña D, Álvarez-Meza AM, Dolph CV, Iftekharuddin KM, Eskildsen SF, Coupé P, Fonov VS, Franke K, Gaser C, Ledig C, Guerrero R, Tong T, Gray KR, Moradi E, Tohka J, Routier A, Durrleman S, Sarica A, Di Fatta G, Sensi F, Chincarini A, Smith GM, Stoyanov ZV, Sørensen L, Nielsen M, Tangaro S, Inglese P, Wachinger C, Reuter M, van Swieten JC, Niessen WJ, Klein S. Standardized evaluation of algorithms for computer-aided diagnosis of dementia based on structural MRI: The CADDementia challenge. NeuroImage. 2015.

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Reuter M, Tisdall MD, Qureshi A, Buckner RL, van der Kouwe AJW, Fischl B. Head motion during MRI acquisition reduces gray matter volume and thickness estimates. NeuroImage. 2015.

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Wachinger C, Golland P, Magnain C, Fischl B, Reuter M. Multi-Modal Robust Inverse-Consistent Linear Registration. Hum Brain Mapp. 2015.

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Aganj I, Reuter M, Sabuncu MR, Fischl B. Avoiding symmetry-breaking spatial non-uniformity in deformable image registration via a quasi-volume-preserving constraint. NeuroImage. 2015.

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Wachinger C, Golland P, Reuter M. BrainPrint : Identifying Subjects by Their Brain. MICCAI. 2014.

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Wachinger C, Batmanghelich K, Golland P, Reuter M. BrainPrint in the Computer-Aided Diagnosis of Alzheimer’s Disease. MICCAI Challenge on Computer-Aided Diagnosis of Dementia Based on Structural MRI Data. 2014.

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Wachinger C, Golland P, Reuter M, Wells W. Gaussian process interpolation for uncertainty estimation in image registration. MICCAI. 2014.

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Wade BS, Joshi SH, Reuter M, Blumenthal JD, Toga AW, Thompson PM, Giedd JN. Effects of sex chromosome dosage on corpus callosum morphology in supernumerary sex chromosome aneuploidies. Biol Sex Differ. 2014.

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Wang H, Zhu J, Reuter M, Vinke LN, Yendiki A, Boas DA, Fischl B, Akkin T. Cross-validation of serial optical coherence scanning and diffusion tensor imaging: a study on neural fiber maps in human medulla oblongata. NeuroImage. 2014.

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Sabuncu MR, Bernal-Rusiel JL, Reuter M, Greve DN, Fischl B. Event time analysis of longitudinal neuroimage data. NeuroImage. 2014.

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Reuter M, Gerstner ER, Rapalino O, Batchelor TT, Rosen B, Fischl B. Impact of MRI head placement on glioma response assessment. J Neurooncol. 2014.

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Augustinack JC, Magnain C, Reuter M, van der Kouwe AJW, Boas D, Fischl B. MRI Parcellation of Ex Vivo Medial Temporal Lobe. NeuroImage. 2014.

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Andronesi OC, Bhat H, Reuter M, Mukherjee S, Caravan P, Rosen BR. Whole brain mapping of water pools and molecular dynamics with rotating frame MR relaxation using gradient modulated low-power adiabatic pulses. NeuroImage. 2014.

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Fujimoto K, Polimeni JR, van der Kouwe AJW, Reuter M, Kober T, Benner T, Fischl B, Wald LL. Quantitative comparison of cortical surface reconstructions from MP2RAGE and multi-echo MPRAGE data at 3 and 7 T. NeuroImage. 2014.

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Adriaanse SM, Dijk KRA, Ossenkoppele R, Reuter M, Tolboom N, Zwan MD, Yaqub M, Boellaard R, Windhorst AD, Flier WM, Scheltens, P, Lammertsma AA, Barkhof F, Berckel BNM. The effect of amyloid pathology and glucose metabolism on cortical volume loss over time in Alzheimer’s disease. European Journal of Nuclear Medicine and Molecular Imaging. 2014.

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Rosas HD, Doros G, Gevorkian S, Malarick K, Reuter M, Coutu JP, Triggs T, Wilkens P, Matson W, Salat DH, Hersch SM. PRECREST: A phase II prevention and biomarker trial of creatine in at-risk Huntington disease. Neurology. 2014.

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Magnain C, Augustinack JC, Reuter M, Wachinger C, Frosch MP, Ragan T, Akkin T, Wedeen VJ, Boas DA, Fischl B. Blockface histology with optical coherence tomography: A comparison with Nissl staining. NeuroImage. 2014.

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Bernal-Rusiel JL, Reuter M, Greve DN, Fischl B, Sabuncu MR. Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate Analysis of Longitudinal Neuroimage Data. NeuroImage. 2013.

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Aganj I, Reuter M, Sabuncu MR, Fischl B. Symmetric non-rigid image registration via an adaptive quasi-volume-preserving constraint. ISBI. 2013.

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Bernal-Rusiel JL, Greve DN, Reuter M, Fischl B, Sabuncu MR. Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models. NeuroImage. 2013.

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Lian Z, Godil A, Bustos B, Daoudi M, Hermans J, Kawamura S, Kurita Y, Lavoué G, Van Nguyen H, Ohbuchi R, Ohkita Y, Ohishi Y, Porikli F, Reuter M, Sipiran I, Smeets D, Suetens P, Tabia H, Vandermeulen D. A comparison of methods for non-rigid 3D shape retrieval. Pattern Recognition. 2013.

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Tisdall MD, Hess AT, Reuter M, and Meintjes EM, Fischl B, van der Kouwe AJW. Volumetric navigators for prospective motion correction and selective reacquisition in neuroanatomical MRI. Magnetic Resonance in Medicine. 2012.

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Adriaanse S, van Dijk K, Ossenkoppele R, Reuter M, Tolboom N, Zwan M, Yaqub M, Boellaard R, Windhorst A, Van der Flier W, Scheltens, P, Barkhof F, Lammertsma A, van Berckel B. Exploring the biomarker cascade model: Relating cortical volume loss to [11C]PIB, [18F]FDG and MMSE over time in Alzheimer’s disease patients and normal controls. Alzheimer’s & Dementia. 2012.

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Reuter M, Schmansky NJ, Rosas HD, Fischl B. Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis. NeuroImage. 2012.

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Rosas HD, Reuter M, Doros G, Lee SY, Triggs T, Malarick K, Fischl B, Salat DH, Hersch SM. A tale of two factors: What determines the rate of progression in Huntington’s disease? A longitudinal MRI study. Movement Disorders. 2011.

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Sabuncu MR, Desikan RS, Sepulcre J, Yeo BTT, Liu H, Schmansky NJ, Reuter M, Weiner MW, Buckner RL, Sperling RA, Fischl B, Alzheimer’s Disease Neuroimaging Initiative. The Dynamics of Cortical and Hippocampal Atrophy in Alzheimer Disease. Arch Neurol.. 2011.

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Reuter M, Fischl B. Avoiding Asymmetry-Induced Bias in Longitudinal Image Processing. NeuroImage. 2011.

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Lian Z, Godil A, Bustos B, Daoudi M, Hermans J, Kawamura S, Kurita Y, Lavoué G, Nguyen HV, Ohbuchi R, Ohkita Y, Ohishi Y, Porikli F, Reuter M, Sipiran I, Smeets D, Suetens P, Tabia H, Vandermeulen D. SHREC’11 track: shape retrieval on non-rigid 3D watertight meshes. Eurographics - 3DOR’11 Workshop. 2011.

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Desikan RS, Sabuncu MR, Schmansky NJ, Reuter M, Cabral HJ, Hess CP, Weiner MW, Biffi A, Anderson CD, Rosand J, Salat DH, Kemper TL, Dale AM, Sperling RA, Fischl B, Alzheimer’s Disease Neuroimaging Initiative. Seletive Disruption of the Cerebral Neocortex in Alzheimer’s Disease. PLoS ONE. 2010.

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Reuter M, Rosas HD, Fischl B. Highly Accurate Inverse Consistent Registration: A Robust Approach. NeuroImage. 2010.

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Reuter M. Hierarchical Shape Segmentation and Registration via Topological Features of Laplace-Beltrami Eigenfunctions. International Journal of Computer Vision. 2010.

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Reuter M, Biasotti S, Giorgi D, Patanè G, Spagnuolo M. Discrete Laplace-Beltrami operators for shape analysis and segmentation. Computers & Graphics. 2009.

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Reuter M, Wolter FE, Shenton M, Niethammer M. Laplace-Beltrami Eigenvalues and Topological Features of Eigenfunctions for Statistical Shape Analysis. Computer-Aided Design. 2009.

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Reuter M, Mikkelsen TS, Sherbrooke EC, Maekawa T, Patrikalakis NM. Solving nonlinear polynomial systems in the barycentric Bernstein basis. The Visual Computer. 2008.

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Reuter M. Can one hear Shape?. GAMM07 and ICIAM07. 2007.

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Reuter M, Niethammer M, Wolter FE, Bouix S, Shenton M. Global Medical Shape Analysis Using the Volumetric Laplace Spectrum. CW. 2007.

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Niethammer M, Reuter M, Wolter FE, Bouix S, Peinecke N, Koo MS, Shenton M. Global Medical Shape Analysis using the Laplace-Beltrami Spectrum. MICCAI. 2007.

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Wolter FE, Reuter M, Peinecke N. Geometric Modeling for Engineering Applications. Encyclopedia of Computational Mechanics. 2007.

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Peinecke N, Wolter FE, Reuter M. Laplace Spectra as Fingerprints for Image Recognition. Computer-Aided Design. 2007.

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Reuter M. Laplace Spectra for Shape Recognition. BoD. 2006.

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Reuter M, Wolter FE, Peinecke N. Laplace-Beltrami spectra as “Shape-DNA” of surfaces and solids. Computer-Aided Design. 2006.

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Reuter M, Wolter FE, Peinecke N. Laplace-Spectra as Fingerprints for Shape Matching. SPM. 2005.

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Wolter FE, Peinecke N, Reuter M. Geometric Modeling of Complex Shapes and Engineering Artifacts. Encyclopedia of Computational Mechanics. 2004.

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