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Ferreira M, Schaprian T, Kügler D, Reuter M, Deike-Hoffmann K, Timmann D, Ernst TM, Giunti P, Garcia-Moreno H, van de Warrenburg B, van Gaalen J, de Vries J, Jacobi H, Steiner KM, Öz G, Joers JM, Onyike C, Povazan M, Reetz K, Romanzetti S, Klockgether T, Faber J. Correction: Cerebellar Volumetry in Ataxias: Relation to Ataxia Severity and Duration. Cerebellum 2024:10.1007/s12311-024-01681-2. [PMID: 38446346 DOI: 10.1007/s12311-024-01681-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Affiliation(s)
- Mónica Ferreira
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- University of Bonn, Bonn, Germany
| | - Tamara Schaprian
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - David Kügler
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Martin Reuter
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | | | - Dagmar Timmann
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Thomas M Ernst
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Judith van Gaalen
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Neurology Department, Rijnstate Hospital, Arnhem, The Netherlands
| | - Jeroen de Vries
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Heike Jacobi
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Katharina Marie Steiner
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Gülin Öz
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA
| | - James M Joers
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA
| | - Chiadi Onyike
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michal Povazan
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kathrin Reetz
- Department of Neurology, RWTH Aachen University, Aachen, Germany
- JARA-Brain Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich, Jülich, Germany
| | | | - Thomas Klockgether
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University Hospital Bonn, Bonn, Germany
| | - Jennifer Faber
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- Department of Neurology, University Hospital Bonn, Bonn, Germany.
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Ferreira M, Schaprian T, Kügler D, Reuter M, Deike-Hoffmann K, Timmann D, Ernst TM, Giunti P, Garcia-Moreno H, van de Warrenburg B, van Gaalen J, de Vries J, Jacobi H, Steiner KM, Öz G, Joers JM, Onyike C, Povazan M, Reetz K, Romanzetti S, Klockgether T, Faber J. Cerebellar Volumetry in Ataxias: Relation to Ataxia Severity and Duration. Cerebellum 2024:10.1007/s12311-024-01659-0. [PMID: 38363498 DOI: 10.1007/s12311-024-01659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/15/2024] [Indexed: 02/17/2024]
Abstract
Cerebellar atrophy is the neuropathological hallmark of most ataxias. Hence, quantifying the volume of the cerebellar grey and white matter is of great interest. In this study, we aim to identify volume differences in the cerebellum between spinocerebellar ataxia type 1 (SCA1), SCA3 and SCA6 as well as multiple system atrophy of cerebellar type (MSA-C). Our cross-sectional data set comprised mutation carriers of SCA1 (N=12), SCA3 (N=62), SCA6 (N=14), as well as MSA-C patients (N=16). Cerebellar volumes were obtained from T1-weighted magnetic resonance images. To compare the different atrophy patterns, we performed a z-transformation and plotted the intercept of each patient group's model at the mean of 7 years of ataxia duration as well as at the mean ataxia severity of 14 points in the SARA sum score. In addition, we plotted the extrapolation at ataxia duration of 0 years as well as 0 points in the SARA sum score. Patients with MSA-C demonstrated the most pronounced volume loss, particularly in the cerebellar white matter, at the late time intercept. Patients with SCA6 showed a pronounced volume loss in cerebellar grey matter with increasing ataxia severity compared to all other patient groups. MSA-C, SCA1 and SCA3 showed a prominent atrophy of the cerebellar white matter. Our results (i) confirmed SCA6 being considered as a pure cerebellar grey matter disease, (ii) emphasise the involvement of cerebellar white matter in the neuropathology of SCA1, SCA3 and MSA-C, and (iii) reflect the rapid clinical progression in MSA-C.
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Affiliation(s)
- Mónica Ferreira
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Rhenish Friedrich Wilhelm University of Bonn, Bonn, Germany
| | - Tamara Schaprian
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - David Kügler
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Martin Reuter
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | | | - Dagmar Timmann
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Thomas M Ernst
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Judith van Gaalen
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Neurology Department, Rijnstate Hospital, Arnhem, The Netherlands
| | - Jeroen de Vries
- Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Heike Jacobi
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Katharina Marie Steiner
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Gülin Öz
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA
| | - James M Joers
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA
| | - Chiadi Onyike
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michal Povazan
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kathrin Reetz
- Department of Neurology, RWTH Aachen University, Aachen, Germany
- JARA-Brain Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich, Jülich, Germany
| | | | - Thomas Klockgether
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University Hospital Bonn, Bonn, Germany
| | - Jennifer Faber
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
- Department of Neurology, University Hospital Bonn, Bonn, Germany.
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Ferreira M, Schaprian T, Kügler D, Reuter M, Deike-Hoffmann K, Timmann D, Ernst TM, Giunti P, Garcia-Moreno H, van de Warrenburg B, van Gaalen J, de Vries J, Jacobi H, Steiner KM, Öz G, Joers JM, Onyike C, Povazan M, Reetz K, Romanzetti S, Klockgether T, Faber J. Cerebellar volumetry in ataxias: Relation to ataxia severity and duration. Res Sq 2023:rs.3.rs-3605029. [PMID: 38014351 PMCID: PMC10680914 DOI: 10.21203/rs.3.rs-3605029/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Background Cerebellar atrophy is the neuropathological hallmark of most ataxias. Hence, quantifying the volume of the cerebellar grey and white matter is of great interest. In this study, we aim to identify volume differences in the cerebellum between spinocerebellar ataxia type 1 (SCA1), SCA3 and SCA6 as well as multiple system atrophy of cerebellar type (MSA-C). Methods Our cross-sectional data set comprised mutation carriers of SCA1 (N=12), SCA3 (N=62), SCA6 (N=14), as well as MSA-C patients (N=16). Cerebellar volumes were obtained from T1-weighted magnetic resonance images. To compare the different atrophy patterns, we performed a z-transformation and plotted the intercept of each patient group's model at the mean of 7 years of ataxia duration as well as at the mean ataxia severity of 14 points in the SARA sum score. In addition, we plotted the extrapolation at ataxia duration of 0 years as well as 0 points in the SARA sum score. Results Patients with MSA-C demonstrated the most pronounced volume loss, particularly in the cerebellar white matter, at the late time intercept. Patients with SCA6 showed a pronounced volume loss in cerebellar grey matter with increasing ataxia severity compared to all other patient groups. MSA-C, SCA1 and SCA3 showed a prominent atrophy of the cerebellar white matter. Conclusion Our results (i) confirmed SCA6 being considered as a pure cerebellar gray matter disease, (ii) emphasise the involvement of cerebellar white matter in the neurophatology of SCA1, SCA3 and MSA-C, and (iii) reflect the rapid clinical progression in MSA-C.
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Affiliation(s)
- Mónica Ferreira
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Tamara Schaprian
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - David Kügler
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Martin Reuter
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, U.S
- Department of Radiology, Harvard Medical School, Boston, MA, U.S
| | | | - Dagmar Timmann
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Thomas M Ernst
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Judith van Gaalen
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
- Neurology department, Rijnstate Hospital, Arnhem, the Netherlands
| | - Jeroen de Vries
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Heike Jacobi
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Katharina Marie Steiner
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen, Germany
| | - Gülin Öz
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA
| | - James M Joers
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA
| | - Chiadi Onyike
- Johns Hopkins University School of Medicine, Baltimore, MD, U.S
| | - Michal Povazan
- Johns Hopkins University School of Medicine, Baltimore, MD, U.S
| | - Kathrin Reetz
- Department of Neurology, RWTH Aachen University, Germany
- JARA-Brain Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich, Germany
| | | | - Thomas Klockgether
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University Hospital Bonn, Germany
| | - Jennifer Faber
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Neurology, University Hospital Bonn, Germany
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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; 275:120176. [PMID: 37209757 DOI: 10.1016/j.neuroimage.2023.120176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/22/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023] Open
Abstract
Head motion during MR acquisition reduces image quality and has been shown to bias neuromorphometric analysis. The quantification of head motion, therefore, has both neuroscientific as well as clinical applications, for example, to control for motion in statistical analyses of brain morphology, or as a variable of interest in neurological studies. The accuracy of markerless optical head tracking, however, is largely unexplored. Furthermore, no quantitative analysis of head motion in a general, mostly healthy population cohort exists thus far. In this work, we present a robust registration method for the alignment of depth camera data that sensitively estimates even small head movements of compliant participants. Our method outperforms the vendor-supplied method in three validation experiments: 1. similarity to fMRI motion traces as a low-frequency reference, 2. recovery of the independently acquired breathing signal as a high-frequency reference, and 3. correlation with image-based quality metrics in structural T1-weighted MRI. In addition to the core algorithm, we establish an analysis pipeline that computes average motion scores per time interval or per sequence for inclusion in downstream analyses. We apply the pipeline in the Rhineland Study, a large population cohort study, where we replicate age and body mass index (BMI) as motion correlates and show that head motion significantly increases over the duration of the scan session. We observe weak, yet significant interactions between this within-session increase and age, BMI, and sex. High correlations between fMRI and camera-based motion scores of proceeding sequences further suggest that fMRI motion estimates can be used as a surrogate score in the absence of better measures to control for motion in statistical analyses.
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Affiliation(s)
- Clemens Pollak
- AI in Medical Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - David Kügler
- AI in Medical Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Monique M B Breteler
- Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Martin Reuter
- AI in Medical Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA.
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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, Reuter M, Garcia-Moreno H, Jacobi H, Jende J, de Vries J, Povazan M, Barker PB, Steiner KM, Krahe J. CerebNet: A fast and reliable deep-learning pipeline for detailed cerebellum sub-segmentation. Neuroimage 2022; 264:119703. [PMID: 36349595 PMCID: PMC9771831 DOI: 10.1016/j.neuroimage.2022.119703] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022] Open
Abstract
Quantifying the volume of the cerebellum and its lobes is of profound interest in various neurodegenerative and acquired diseases. Especially for the most common spinocerebellar ataxias (SCA), for which the first antisense oligonculeotide-base gene silencing trial has recently started, there is an urgent need for quantitative, sensitive imaging markers at pre-symptomatic stages for stratification and treatment assessment. This work introduces CerebNet, a fully automated, extensively validated, deep learning method for the lobular segmentation of the cerebellum, including the separation of gray and white matter. For training, validation, and testing, T1-weighted images from 30 participants were manually annotated into cerebellar lobules and vermal sub-segments, as well as cerebellar white matter. CerebNet combines FastSurferCNN, a UNet-based 2.5D segmentation network, with extensive data augmentation, e.g. realistic non-linear deformations to increase the anatomical variety, eliminating additional preprocessing steps, such as spatial normalization or bias field correction. CerebNet demonstrates a high accuracy (on average 0.87 Dice and 1.742mm Robust Hausdorff Distance across all structures) outperforming state-of-the-art approaches. Furthermore, it shows high test-retest reliability (average ICC >0.97 on OASIS and Kirby) as well as high sensitivity to disease effects, including the pre-ataxic stage of spinocerebellar ataxia type 3 (SCA3). CerebNet is compatible with FreeSurfer and FastSurfer and can analyze a 3D volume within seconds on a consumer GPU in an end-to-end fashion, thus providing an efficient and validated solution for assessing cerebellum sub-structure volumes. We make CerebNet available as source-code (https://github.com/Deep-MI/FastSurfer).
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Affiliation(s)
- Jennifer Faber
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany,Department of Neurology, University Hospital Bonn, Germany
| | - David Kügler
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Emad Bahrami
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany,Computer Science Department, University Bonn, Bonn, Germany
| | - Lea-Sophie Heinz
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dagmar Timmann
- Department of Neurology, Center for Translational Neuro, and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Thomas M. Ernst
- Department of Neurology, Center for Translational Neuro, and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Thomas Klockgether
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany,Department of Neurology, University Hospital Bonn, Germany
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Judith van Gaalen
- Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Kathrin Reetz
- Department of Neurology, RWTH Aachen University, Germany,JARA-Brain Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich, Germany
| | | | - Gulin Oz
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA
| | - James M. Joers
- Center for Magnetic Resonance Research, Department of Radiology, University of Minnesota, Minneapolis, MN, USA
| | - Jorn Diedrichsen
- Departments of Computer Science and Statistical and Actuarial Sciences, Western University, London, ON, Canada
| | - ESMI MRI Study GroupGiuntiPaola1Garcia-MorenoHector1JacobiHeike3JendeJohann4de VriesJeroen5PovazanMichal6BarkerPeter B.6SteinerKatherina Marie8KraheJanna9Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology & National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UKDepartment of Neurology, University Hospital of Heidelberg, Heidelberg, GermanyDepartment of Neuroradiology, Heidelberg University Hospital, Heidelberg, GermanyDepartment of Neurology, Expertise Center Movement Disorders Groningen, University Medical Center Groningen, University of Groningen, The NetherlandsJohns Hopkins University School of Medicine, Baltimore, MD, U.S.Department of Neurology, Center for Translational Neuro, and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, GermanyDepartment of Neurology, RWTH Aachen University, Germany
| | - Martin Reuter
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA,Department of Radiology, Harvard Medical School, Boston, MA, USA,Corresponding author.
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Henschel L, Kügler D, Reuter M. FastSurferVINN: Building resolution-independence into deep learning segmentation methods-A solution for HighRes brain MRI. Neuroimage 2022; 251:118933. [PMID: 35122967 PMCID: PMC9801435 DOI: 10.1016/j.neuroimage.2022.118933] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/22/2021] [Accepted: 01/24/2022] [Indexed: 01/04/2023] Open
Abstract
Leading neuroimaging studies have pushed 3T MRI acquisition resolutions below 1.0 mm for improved structure definition and morphometry. Yet, only few, time-intensive automated image analysis pipelines have been validated for high-resolution (HiRes) settings. Efficient deep learning approaches, on the other hand, rarely support more than one fixed resolution (usually 1.0 mm). Furthermore, the lack of a standard submillimeter resolution as well as limited availability of diverse HiRes data with sufficient coverage of scanner, age, diseases, or genetic variance poses additional, unsolved challenges for training HiRes networks. Incorporating resolution-independence into deep learning-based segmentation, i.e., the ability to segment images at their native resolution across a range of different voxel sizes, promises to overcome these challenges, yet no such approach currently exists. We now fill this gap by introducing a Voxel-size Independent Neural Network (VINN) for resolution-independent segmentation tasks and present FastSurferVINN, which (i) establishes and implements resolution-independence for deep learning as the first method simultaneously supporting 0.7-1.0 mm whole brain segmentation, (ii) significantly outperforms state-of-the-art methods across resolutions, and (iii) mitigates the data imbalance problem present in HiRes datasets. Overall, internal resolution-independence mutually benefits both HiRes and 1.0 mm MRI segmentation. With our rigorously validated FastSurferVINN we distribute a rapid tool for morphometric neuroimage analysis. The VINN architecture, furthermore, represents an efficient resolution-independent segmentation method for wider application.
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Affiliation(s)
- Leonie Henschel
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - David Kügler
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Martin Reuter
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA; Department of Radiology, Harvard Medical School, Boston, MA, USA.
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Kügler D, Sehring J, Stefanov A, Stenin I, Kristin J, Klenzner T, Schipper J, Mukhopadhyay A. i3PosNet: instrument pose estimation from X-ray in temporal bone surgery. Int J Comput Assist Radiol Surg 2020; 15:1137-1145. [PMID: 32440956 PMCID: PMC7316684 DOI: 10.1007/s11548-020-02157-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/03/2020] [Indexed: 11/03/2022]
Abstract
PURPOSE Accurate estimation of the position and orientation (pose) of surgical instruments is crucial for delicate minimally invasive temporal bone surgery. Current techniques lack in accuracy and/or line-of-sight constraints (conventional tracking systems) or expose the patient to prohibitive ionizing radiation (intra-operative CT). A possible solution is to capture the instrument with a c-arm at irregular intervals and recover the pose from the image. METHODS i3PosNet infers the position and orientation of instruments from images using a pose estimation network. Said framework considers localized patches and outputs pseudo-landmarks. The pose is reconstructed from pseudo-landmarks by geometric considerations. RESULTS We show i3PosNet reaches errors [Formula: see text] mm. It outperforms conventional image registration-based approaches reducing average and maximum errors by at least two thirds. i3PosNet trained on synthetic images generalizes to real X-rays without any further adaptation. CONCLUSION The translation of deep learning-based methods to surgical applications is difficult, because large representative datasets for training and testing are not available. This work empirically shows sub-millimeter pose estimation trained solely based on synthetic training data.
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Affiliation(s)
- David Kügler
- Department of Computer Science, Technischer Universität Darmstadt, Darmstadt, Germany. .,German Center for Degenerative Diseases (DZNE) e.V., Bonn, Germany.
| | - Jannik Sehring
- Department of Computer Science, Technischer Universität Darmstadt, Darmstadt, Germany
| | - Andrei Stefanov
- Department of Computer Science, Technischer Universität Darmstadt, Darmstadt, Germany
| | - Igor Stenin
- ENT Clinic, University Düsseldorf, Düsseldorf, Germany
| | - Julia Kristin
- ENT Clinic, University Düsseldorf, Düsseldorf, Germany
| | | | - Jörg Schipper
- ENT Clinic, University Düsseldorf, Düsseldorf, Germany
| | - Anirban Mukhopadhyay
- Department of Computer Science, Technischer Universität Darmstadt, Darmstadt, Germany
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Kügler D, Krumb H, Bredemann J, Stenin I, Kristin J, Klenzner T, Schipper J, Schmitt R, Sakas G, Mukhopadhyay A. High-precision evaluation of electromagnetic tracking. Int J Comput Assist Radiol Surg 2019; 14:1127-1135. [PMID: 30982148 DOI: 10.1007/s11548-019-01959-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/01/2019] [Indexed: 01/26/2023]
Abstract
PURPOSE Navigation in high-precision minimally invasive surgery (HP-MIS) demands high tracking accuracy in the absence of line of sight (LOS). Currently, no tracking technology can satisfy this requirement. Electromagnetic tracking (EMT) is the best tracking paradigm in the absence of LOS despite limited accuracy and robustness. Novel evaluation protocols are needed to ensure high-precision and robust EMT for navigation in HP-MIS. METHODS We introduce a novel protocol for EMT measurement evaluation featuring a high-accuracy phantom based on LEGO[Formula: see text], which is calibrated by a coordinate measuring machine to ensure accuracy. Our protocol includes relative sequential positions and an uncertainty estimation of positioning. We show effects on distortion compensation using a learned interpolation model. RESULTS Our high-precision protocol clarifies properties of errors and uncertainties of EMT for high-precision use cases. For EMT errors reaching clinically relevant 0.2 mm, our design is 5-10 times more accurate than previous protocols with 95% confidence margins of 0.02 mm. This high-precision protocol ensures the performance improvement in compensated EMT by 0.05 mm. CONCLUSION Our protocol improves the reliability of EMT evaluations because of significantly lower protocol-inherent uncertainties. To reduce patient risk in HP-MIS and to evaluate magnetic field distortion compensation, more high-accuracy protocols such as the one proposed here are required.
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Affiliation(s)
- David Kügler
- Department of Computer Science, Technischer Universität Darmstadt, Darmstadt, Germany.
| | - Henry Krumb
- Department of Computer Science, Technischer Universität Darmstadt, Darmstadt, Germany
| | | | - Igor Stenin
- ENT Clinic, University Düsseldorf, Düsseldorf, Germany
| | - Julia Kristin
- ENT Clinic, University Düsseldorf, Düsseldorf, Germany
| | | | - Jörg Schipper
- ENT Clinic, University Düsseldorf, Düsseldorf, Germany
| | | | - Georgios Sakas
- Department of Computer Science, Technischer Universität Darmstadt, Darmstadt, Germany
| | - Anirban Mukhopadhyay
- Department of Computer Science, Technischer Universität Darmstadt, Darmstadt, Germany
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Kügler D, Müller K, Barth J. Toxische Pneumonitis bei Feuerschluckern. Pneumologie 2006. [DOI: 10.1055/s-2006-933887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Kügler D, Jäger D, Barth J. A patient with pancreatitis, anaemia and an intrathoracic tumour. Diagnosis: tumour-simulating asymptomatic intrathoracic extramedullary haematopoiesis (EMH) in a patient with hereditary spherocytosis. Eur Respir J 2006; 27:856-9. [PMID: 16585094 DOI: 10.1183/09031936.06.00105905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D Kügler
- Medizinische Klinik, BG Kliniken Bergmannstrost, Merseburger Str. 165, 06112 Halle/Saale, Germany.
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Kügler D, Holzhausen HJ. [Historical development of grading of malignant soft tissue tumors]. Sudhoffs Arch 2002; 85:45-54. [PMID: 11505727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
This article describes the historical development of the grading systems for malignant soft tissue tumors. First attempts to grade these tumors were made in the middle of the nineteenth century; a remarkable amount of activity in grading took place in the 1970s with an apex in the 1980s. Reviewing the literature back to the first available publications, five phases in the development of the grading systems for malignant soft tissue tumors could be distinguished: 1845-1919: phase of identification, 1927-1964: phase of description, 1965-1977: phase of predominant mitotic activity, 1979-1983: phase of predominant tumor type, from 1984: phase of multifactorial systems.
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Affiliation(s)
- D Kügler
- Medizinische Klinik BG Kliniken Bergmannstrost Merseburger Str. 165 06112 Halle/S.
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Abstract
This article describes the historical development of the grading systems for malignant soft tissue tumors. The first attempts to grade these tumors were made in the middle of the nineteen century; a remarkable amount of activity in grading took place in the 1970s which reached a maximum in the 1980s. Reviewing the literature back to the first available publications, five phases in the development of the grading systems for malignant soft tissue tumors could be distinguished. Five commonly used systems were checked for comparing and handling of 339 patients with malignant soft tissue tumors. The use of two multifactorial systems, one simple and one complex, to grade malignant soft tissue tumors should be favored.
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Affiliation(s)
- D Kügler
- Institut für Pathologie, Martin-Luther-Universität Halle-Wittenberg
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Kügler D, Wettengel R. [Theophylline in allergic bronchial asthma (author's transl)]. Prax Klin Pneumol 1982; 36:27-32. [PMID: 7048279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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