White matter hyperintensity quantification in large-scale clinical acute ischemic stroke cohorts – The MRI-GENIE study
White matter hyperintensity (WMH) burden is a critically important cerebrovascular phenotype linked to prediction of diagnosis and prognosis of diseases, such as acute ischemic stroke (AIS). However, current approaches to its quantification on clinical MRI often rely on time intensive manual delinea...
| Main Authors: | , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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Elsevier BV
2021
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| Online Access: | https://hdl.handle.net/1721.1/129570 |
| _version_ | 1811093723908407296 |
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| author | Schirmer, Markus Dalca, Adrian Vasile Sridharan, Ramesh Golland, Polina |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Schirmer, Markus Dalca, Adrian Vasile Sridharan, Ramesh Golland, Polina |
| author_sort | Schirmer, Markus |
| collection | MIT |
| description | White matter hyperintensity (WMH) burden is a critically important cerebrovascular phenotype linked to prediction of diagnosis and prognosis of diseases, such as acute ischemic stroke (AIS). However, current approaches to its quantification on clinical MRI often rely on time intensive manual delineation of the disease on T2 fluid attenuated inverse recovery (FLAIR), which hinders high-throughput analyses such as genetic discovery. In this work, we present a fully automated pipeline for quantification of WMH in clinical large-scale studies of AIS. The pipeline incorporates automated brain extraction, intensity normalization and WMH segmentation using spatial priors. We first propose a brain extraction algorithm based on a fully convolutional deep learning architecture, specifically designed for clinical FLAIR images. We demonstrate that our method for brain extraction outperforms two commonly used and publicly available methods on clinical quality images in a set of 144 subject scans across 12 acquisition centers, based on dice coefficient (median 0.95; inter-quartile range 0.94–0.95; p < 0.01) and Pearson correlation of total brain volume (r = 0.90). Subsequently, we apply it to the large-scale clinical multi-site MRI-GENIE study (N = 2783) and identify a decrease in total brain volume of −2.4 cc/year. Additionally, we show that the resulting total brain volumes can successfully be used for quality control of image preprocessing. Finally, we obtain WMH volumes by building on an existing automatic WMH segmentation algorithm that delineates and distinguishes between different cerebrovascular pathologies. The learning method mimics expert knowledge of the spatial distribution of the WMH burden using a convolutional auto-encoder. This enables successful computation of WMH volumes of 2533 clinical AIS patients. We utilize these results to demonstrate the increase of WMH burden with age (0.950 cc/year) and show that single site estimates can be biased by the number of subjects recruited. |
| first_indexed | 2024-09-23T15:49:37Z |
| format | Article |
| id | mit-1721.1/129570 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T15:49:37Z |
| publishDate | 2021 |
| publisher | Elsevier BV |
| record_format | dspace |
| spelling | mit-1721.1/1295702022-09-29T16:25:39Z White matter hyperintensity quantification in large-scale clinical acute ischemic stroke cohorts – The MRI-GENIE study Schirmer, Markus Dalca, Adrian Vasile Sridharan, Ramesh Golland, Polina Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science White matter hyperintensity (WMH) burden is a critically important cerebrovascular phenotype linked to prediction of diagnosis and prognosis of diseases, such as acute ischemic stroke (AIS). However, current approaches to its quantification on clinical MRI often rely on time intensive manual delineation of the disease on T2 fluid attenuated inverse recovery (FLAIR), which hinders high-throughput analyses such as genetic discovery. In this work, we present a fully automated pipeline for quantification of WMH in clinical large-scale studies of AIS. The pipeline incorporates automated brain extraction, intensity normalization and WMH segmentation using spatial priors. We first propose a brain extraction algorithm based on a fully convolutional deep learning architecture, specifically designed for clinical FLAIR images. We demonstrate that our method for brain extraction outperforms two commonly used and publicly available methods on clinical quality images in a set of 144 subject scans across 12 acquisition centers, based on dice coefficient (median 0.95; inter-quartile range 0.94–0.95; p < 0.01) and Pearson correlation of total brain volume (r = 0.90). Subsequently, we apply it to the large-scale clinical multi-site MRI-GENIE study (N = 2783) and identify a decrease in total brain volume of −2.4 cc/year. Additionally, we show that the resulting total brain volumes can successfully be used for quality control of image preprocessing. Finally, we obtain WMH volumes by building on an existing automatic WMH segmentation algorithm that delineates and distinguishes between different cerebrovascular pathologies. The learning method mimics expert knowledge of the spatial distribution of the WMH burden using a convolutional auto-encoder. This enables successful computation of WMH volumes of 2533 clinical AIS patients. We utilize these results to demonstrate the increase of WMH burden with age (0.950 cc/year) and show that single site estimates can be biased by the number of subjects recruited. 2021-01-26T16:25:13Z 2021-01-26T16:25:13Z 2019-05 2019-05 2020-12-16T17:13:22Z Article http://purl.org/eprint/type/JournalArticle 2213-1582 https://hdl.handle.net/1721.1/129570 Schirmer, Markus D. et al. “White matter hyperintensity quantification in large-scale clinical acute ischemic stroke cohorts – The MRI-GENIE study.” NeuroImage: Clinical, 23 (May 2019): 101884 © 2019 The Author(s) en 10.1016/J.NICL.2019.101884 NeuroImage: Clinical Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Elsevier BV Elsevier |
| spellingShingle | Schirmer, Markus Dalca, Adrian Vasile Sridharan, Ramesh Golland, Polina White matter hyperintensity quantification in large-scale clinical acute ischemic stroke cohorts – The MRI-GENIE study |
| title | White matter hyperintensity quantification in large-scale clinical acute ischemic stroke cohorts – The MRI-GENIE study |
| title_full | White matter hyperintensity quantification in large-scale clinical acute ischemic stroke cohorts – The MRI-GENIE study |
| title_fullStr | White matter hyperintensity quantification in large-scale clinical acute ischemic stroke cohorts – The MRI-GENIE study |
| title_full_unstemmed | White matter hyperintensity quantification in large-scale clinical acute ischemic stroke cohorts – The MRI-GENIE study |
| title_short | White matter hyperintensity quantification in large-scale clinical acute ischemic stroke cohorts – The MRI-GENIE study |
| title_sort | white matter hyperintensity quantification in large scale clinical acute ischemic stroke cohorts the mri genie study |
| url | https://hdl.handle.net/1721.1/129570 |
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