3D Segmentation of Perivascular Spaces on T1-Weighted 3 Tesla MR Images With a Convolutional Autoencoder and a U-Shaped Neural Network

We implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia (BG). This algorithm is based on an autoencoder and a U-shaped network (U-net), and was trained and tested using T1-weighted magnetic resonance...

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Published in:	Frontiers in neuroinformatics Vol. 15; p. 641600
Main Authors:	Boutinaud, Philippe, Tsuchida, Ami, Laurent, Alexandre, Adonias, Filipa, Hanifehlou, Zahra, Nozais, Victor, Verrecchia, Violaine, Lampe, Leonie, Zhang, Junyi, Zhu, Yi-Cheng, Tzourio, Christophe, Mazoyer, Bernard, Joliot, Marc
Format:	Journal Article
Language:	English
Published:	Switzerland Frontiers Research Foundation 18.06.2021 Frontiers Media Frontiers Media S.A
Subjects:	Algorithms Basal ganglia brain cohort Brain research Cognitive ability Deep learning Dementia Life Sciences Magnetic resonance imaging Medical imaging Medical research MRI Neural networks Neuroscience Performance evaluation perivascular space Santé publique et épidémiologie Segmentation Substantia alba Traumatic brain injury U-net Young adults perivascular space deep learning segmentation brain cohort MRI U-net Deep learning Brain cohort Segmentation Perivascular space
ISSN:	1662-5196, 1662-5196
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Abstract	We implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia (BG). This algorithm is based on an autoencoder and a U-shaped network (U-net), and was trained and tested using T1-weighted magnetic resonance imaging (MRI) data from a large database of 1,832 healthy young adults. An important feature of this approach is the ability to learn from relatively sparse data, which gives the present algorithm a major advantage over other DL algorithms. Here, we trained the algorithm with 40 T1-weighted MRI datasets in which all “visible” PVSs were manually annotated by an experienced operator. After learning, performance was assessed using another set of 10 MRI scans from the same database in which PVSs were also traced by the same operator and were checked by consensus with another experienced operator. The Sorensen-Dice coefficients for PVS voxel detection in DWM (resp. BG) were 0.51 (resp. 0.66), and 0.64 (resp. 0.71) for PVS cluster detection (volume threshold of 0.5 within a range of 0 to 1). Dice values above 0.90 could be reached for detecting PVSs larger than 10 mm 3 and 0.95 for PVSs larger than 15 mm 3 . We then applied the trained algorithm to the rest of the database (1,782 individuals). The individual PVS load provided by the algorithm showed a high agreement with a semi-quantitative visual rating done by an independent expert rater, both for DWM and for BG. Finally, we applied the trained algorithm to an age-matched sample from another MRI database acquired using a different scanner. We obtained a very similar distribution of PVS load, demonstrating the interoperability of this algorithm.
AbstractList	We implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia (BG). This algorithm is based on an autoencoder and a U-shaped network (U-net), and was trained and tested using T1-weighted magnetic resonance imaging (MRI) data from a large database of 1,832 healthy young adults. An important feature of this approach is the ability to learn from relatively sparse data, which gives the present algorithm a major advantage over other DL algorithms. Here, we trained the algorithm with 40 T1-weighted MRI datasets in which all “visible” PVSs were manually annotated by an experienced operator. After learning, performance was assessed using another set of 10 MRI scans from the same database in which PVSs were also traced by the same operator and were checked by consensus with another experienced operator. The Sorensen-Dice coefficients for PVS voxel detection in DWM (resp. BG) were 0.51 (resp. 0.66), and 0.64 (resp. 0.71) for PVS cluster detection (volume threshold of 0.5 within a range of 0 to 1). Dice values above 0.90 could be reached for detecting PVSs larger than 10 mm3 and 0.95 for PVSs larger than 15 mm3. We then applied the trained algorithm to the rest of the database (1,782 individuals). The individual PVS load provided by the algorithm showed a high agreement with a semi-quantitative visual rating done by an independent expert rater, both for DWM and for BG. Finally, we applied the trained algorithm to an age-matched sample from another MRI database acquired using a different scanner. We obtained a very similar distribution of PVS load, demonstrating the interoperability of this algorithm. We implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia (BG). This algorithm is based on an autoencoder and a U-shaped network (U-net), and was trained and tested using T1-weighted magnetic resonance imaging (MRI) data from a large database of 1,832 healthy young adults. An important feature of this approach is the ability to learn from relatively sparse data, which gives the present algorithm a major advantage over other DL algorithms. Here, we trained the algorithm with 40 T1-weighted MRI datasets in which all “visible” PVSs were manually annotated by an experienced operator. After learning, performance was assessed using another set of 10 MRI scans from the same database in which PVSs were also traced by the same operator and were checked by consensus with another experienced operator. The Sorensen-Dice coefficients for PVS voxel detection in DWM (resp. BG) were 0.51 (resp. 0.66), and 0.64 (resp. 0.71) for PVS cluster detection (volume threshold of 0.5 within a range of 0 to 1). Dice values above 0.90 could be reached for detecting PVSs larger than 10 mm 3 and 0.95 for PVSs larger than 15 mm 3 . We then applied the trained algorithm to the rest of the database (1,782 individuals). The individual PVS load provided by the algorithm showed a high agreement with a semi-quantitative visual rating done by an independent expert rater, both for DWM and for BG. Finally, we applied the trained algorithm to an age-matched sample from another MRI database acquired using a different scanner. We obtained a very similar distribution of PVS load, demonstrating the interoperability of this algorithm. We implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia (BG). This algorithm is based on an autoencoder and a U-shaped network (U-net), and was trained and tested using T1-weighted magnetic resonance imaging (MRI) data from a large database of 1,832 healthy young adults. An important feature of this approach is the ability to learn from relatively sparse data, which gives the present algorithm a major advantage over other DL algorithms. Here, we trained the algorithm with 40 T1-weighted MRI datasets in which all "visible" PVSs were manually annotated by an experienced operator. After learning, performance was assessed using another set of 10 MRI scans from the same database in which PVSs were also traced by the same operator and were checked by consensus with another experienced operator. The Sorensen-Dice coefficients for PVS voxel detection in DWM (resp. BG) were 0.51 (resp. 0.66), and 0.64 (resp. 0.71) for PVS cluster detection (volume threshold of 0.5 within a range of 0 to 1). Dice values above 0.90 could be reached for detecting PVSs larger than 10 mm(3) and 0.95 for PVSs larger than 15 mm(3). We then applied the trained algorithm to the rest of the database (1,782 individuals). The individual PVS load provided by the algorithm showed a high agreement with a semi-quantitative visual rating done by an independent expert rater, both for DWM and for BG. Finally, we applied the trained algorithm to an age-matched sample from another MRI database acquired using a different scanner. We obtained a very similar distribution of PVS load, demonstrating the interoperability of this algorithm. We implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia (BG). This algorithm is based on an autoencoder and a U-shaped network (U-net), and was trained and tested using T1-weighted magnetic resonance imaging (MRI) data from a large database of 1,832 healthy young adults. An important feature of this approach is the ability to learn from relatively sparse data, which gives the present algorithm a major advantage over other DL algorithms. Here, we trained the algorithm with 40 T1-weighted MRI datasets in which all "visible" PVSs were manually annotated by an experienced operator. After learning, performance was assessed using another set of 10 MRI scans from the same database in which PVSs were also traced by the same operator and were checked by consensus with another experienced operator. The Sorensen-Dice coefficients for PVS voxel detection in DWM (resp. BG) were 0.51 (resp. 0.66), and 0.64 (resp. 0.71) for PVS cluster detection (volume threshold of 0.5 within a range of 0 to 1). Dice values above 0.90 could be reached for detecting PVSs larger than 10 mm3 and 0.95 for PVSs larger than 15 mm3. We then applied the trained algorithm to the rest of the database (1,782 individuals). The individual PVS load provided by the algorithm showed a high agreement with a semi-quantitative visual rating done by an independent expert rater, both for DWM and for BG. Finally, we applied the trained algorithm to an age-matched sample from another MRI database acquired using a different scanner. We obtained a very similar distribution of PVS load, demonstrating the interoperability of this algorithm.We implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia (BG). This algorithm is based on an autoencoder and a U-shaped network (U-net), and was trained and tested using T1-weighted magnetic resonance imaging (MRI) data from a large database of 1,832 healthy young adults. An important feature of this approach is the ability to learn from relatively sparse data, which gives the present algorithm a major advantage over other DL algorithms. Here, we trained the algorithm with 40 T1-weighted MRI datasets in which all "visible" PVSs were manually annotated by an experienced operator. After learning, performance was assessed using another set of 10 MRI scans from the same database in which PVSs were also traced by the same operator and were checked by consensus with another experienced operator. The Sorensen-Dice coefficients for PVS voxel detection in DWM (resp. BG) were 0.51 (resp. 0.66), and 0.64 (resp. 0.71) for PVS cluster detection (volume threshold of 0.5 within a range of 0 to 1). Dice values above 0.90 could be reached for detecting PVSs larger than 10 mm3 and 0.95 for PVSs larger than 15 mm3. We then applied the trained algorithm to the rest of the database (1,782 individuals). The individual PVS load provided by the algorithm showed a high agreement with a semi-quantitative visual rating done by an independent expert rater, both for DWM and for BG. Finally, we applied the trained algorithm to an age-matched sample from another MRI database acquired using a different scanner. We obtained a very similar distribution of PVS load, demonstrating the interoperability of this algorithm. We implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia (BG). This algorithm is based on an autoencoder and a U-shaped network (U-net), and was trained and tested using T1-weighted magnetic resonance imaging (MRI) data from a large database of 1,832 healthy young adults. An important feature of this approach is the ability to learn from relatively sparse data, which gives the present algorithm a major advantage over other DL algorithms. Here, we trained the algorithm with 40 T1-weighted MRI datasets in which all "visible" PVSs were manually annotated by an experienced operator. After learning, performance was assessed using another set of 10 MRI scans from the same database in which PVSs were also traced by the same operator and were checked by consensus with another experienced operator. The Sorensen-Dice coefficients for PVS voxel detection in DWM (resp. BG) were 0.51 (resp. 0.66), and 0.64 (resp. 0.71) for PVS cluster detection (volume threshold of 0.5 within a range of 0 to 1). Dice values above 0.90 could be reached for detecting PVSs larger than 10 mm and 0.95 for PVSs larger than 15 mm . We then applied the trained algorithm to the rest of the database (1,782 individuals). The individual PVS load provided by the algorithm showed a high agreement with a semi-quantitative visual rating done by an independent expert rater, both for DWM and for BG. Finally, we applied the trained algorithm to an age-matched sample from another MRI database acquired using a different scanner. We obtained a very similar distribution of PVS load, demonstrating the interoperability of this algorithm.
Author	Hanifehlou, Zahra Mazoyer, Bernard Joliot, Marc Laurent, Alexandre Zhu, Yi-Cheng Boutinaud, Philippe Verrecchia, Violaine Nozais, Victor Tsuchida, Ami Lampe, Leonie Tzourio, Christophe Adonias, Filipa Zhang, Junyi
AuthorAffiliation	6 Faculty of Computer Engineering, University of Isfahan , Isfahan , Iran 10 Centre Hospitalier Universitaire de Bordeaux , Bordeaux , France 5 UMR 5293, GIN, IMN, CEA , Bordeaux , France 4 UMR 5293, GIN, IMN, CNRS , Bordeaux , France 8 Department of Neurology, Peking Union Medical College Hospital , Beijing , China 3 UMR 5293, GIN, IMN, Univ. Bordeaux , Bordeaux , France 7 Integrative Model-based Cognitive Neuroscience Research Unit Universiteit van Amsterdam, Amsterdam, Netherlands & Max Planck Institute for Human Cognitive and Brain Sciences Leipzig , Germany 9 U1219, INSERM, Bordeaux Population Health, University Bordeaux , Bordeaux , France 1 Genesislab , Bordeaux , France 2 Fealinx , Lyon , France
AuthorAffiliation_xml	– name: 6 Faculty of Computer Engineering, University of Isfahan , Isfahan , Iran – name: 2 Fealinx , Lyon , France – name: 1 Genesislab , Bordeaux , France – name: 8 Department of Neurology, Peking Union Medical College Hospital , Beijing , China – name: 7 Integrative Model-based Cognitive Neuroscience Research Unit Universiteit van Amsterdam, Amsterdam, Netherlands & Max Planck Institute for Human Cognitive and Brain Sciences Leipzig , Germany – name: 9 U1219, INSERM, Bordeaux Population Health, University Bordeaux , Bordeaux , France – name: 3 UMR 5293, GIN, IMN, Univ. Bordeaux , Bordeaux , France – name: 10 Centre Hospitalier Universitaire de Bordeaux , Bordeaux , France – name: 5 UMR 5293, GIN, IMN, CEA , Bordeaux , France – name: 4 UMR 5293, GIN, IMN, CNRS , Bordeaux , France
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Copyright	Copyright © 2021 Boutinaud, Tsuchida, Laurent, Adonias, Hanifehlou, Nozais, Verrecchia, Lampe, Zhang, Zhu, Tzourio, Mazoyer and Joliot. 2021. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Attribution Copyright © 2021 Boutinaud, Tsuchida, Laurent, Adonias, Hanifehlou, Nozais, Verrecchia, Lampe, Zhang, Zhu, Tzourio, Mazoyer and Joliot. 2021 Boutinaud, Tsuchida, Laurent, Adonias, Hanifehlou, Nozais, Verrecchia, Lampe, Zhang, Zhu, Tzourio, Mazoyer and Joliot
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Keywords	perivascular space deep learning segmentation brain cohort MRI U-net Deep learning Brain cohort Segmentation Perivascular space
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License	Copyright © 2021 Boutinaud, Tsuchida, Laurent, Adonias, Hanifehlou, Nozais, Verrecchia, Lampe, Zhang, Zhu, Tzourio, Mazoyer and Joliot. Attribution: http://creativecommons.org/licenses/by This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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Snippet	We implemented a deep learning (DL) algorithm for the 3-dimensional segmentation of perivascular spaces (PVSs) in deep white matter (DWM) and basal ganglia...
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SubjectTerms	Algorithms Basal ganglia brain cohort Brain research Cognitive ability Deep learning Dementia Life Sciences Magnetic resonance imaging Medical imaging Medical research MRI Neural networks Neuroscience Performance evaluation perivascular space Santé publique et épidémiologie Segmentation Substantia alba Traumatic brain injury U-net Young adults
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Title	3D Segmentation of Perivascular Spaces on T1-Weighted 3 Tesla MR Images With a Convolutional Autoencoder and a U-Shaped Neural Network
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