A Contrast-Agnostic Method for Ultra-High Resolution Claustrum Segmentation
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arXiv
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| Autori principali: | , , , , , , , |
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| Natura: | Preprint |
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2024
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| author | Mauri, Chiara Fritz, Ryan Mora, Jocelyn Billot, Benjamin Iglesias, Juan Eugenio Van Leemput, Koen Augustinack, Jean Greve, Douglas N |
| author_facet | Mauri, Chiara Fritz, Ryan Mora, Jocelyn Billot, Benjamin Iglesias, Juan Eugenio Van Leemput, Koen Augustinack, Jean Greve, Douglas N |
| contents | The claustrum is a band-like gray matter structure located between putamen and insula whose exact functions are still actively researched. Its sheet-like structure makes it barely visible in in vivo Magnetic Resonance Imaging (MRI) scans at typical resolutions and neuroimaging tools for its study, including methods for automatic segmentation, are currently very limited. In this paper, we propose a contrast- and resolution-agnostic method for claustrum segmentation at ultra-high resolution (0.35 mm isotropic); the method is based on the SynthSeg segmentation framework (Billot et al., 2023), which leverages the use of synthetic training intensity images to achieve excellent generalization. In particular, SynthSeg requires only label maps to be trained, since corresponding intensity images are synthesized on the fly with random contrast and resolution. We trained a deep learning network for automatic claustrum segmentation, using claustrum manual labels obtained from 18 ultra-high resolution MRI scans (mostly ex vivo). We demonstrated the method to work on these 18 high resolution cases (Dice score = 0.632, mean surface distance = 0.458 mm, and volumetric similarity = 0.867 using 6-fold Cross Validation (CV)), and also on in vivo T1-weighted MRI scans at typical resolutions (~1 mm isotropic). We also demonstrated that the method is robust in a test-retest setting and when applied to multimodal imaging (T2-weighted, Proton Density and quantitative T1 scans). To the best of our knowledge this is the first accurate method for automatic ultra-high resolution claustrum segmentation, which is robust against changes in contrast and resolution. The method is released at https://github.com/chiara-mauri/claustrum_segmentation and as part of the neuroimaging package Freesurfer (Fischl, 2012). |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2411_15388 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | A Contrast-Agnostic Method for Ultra-High Resolution Claustrum Segmentation Mauri, Chiara Fritz, Ryan Mora, Jocelyn Billot, Benjamin Iglesias, Juan Eugenio Van Leemput, Koen Augustinack, Jean Greve, Douglas N Computer Vision and Pattern Recognition Machine Learning Image and Video Processing The claustrum is a band-like gray matter structure located between putamen and insula whose exact functions are still actively researched. Its sheet-like structure makes it barely visible in in vivo Magnetic Resonance Imaging (MRI) scans at typical resolutions and neuroimaging tools for its study, including methods for automatic segmentation, are currently very limited. In this paper, we propose a contrast- and resolution-agnostic method for claustrum segmentation at ultra-high resolution (0.35 mm isotropic); the method is based on the SynthSeg segmentation framework (Billot et al., 2023), which leverages the use of synthetic training intensity images to achieve excellent generalization. In particular, SynthSeg requires only label maps to be trained, since corresponding intensity images are synthesized on the fly with random contrast and resolution. We trained a deep learning network for automatic claustrum segmentation, using claustrum manual labels obtained from 18 ultra-high resolution MRI scans (mostly ex vivo). We demonstrated the method to work on these 18 high resolution cases (Dice score = 0.632, mean surface distance = 0.458 mm, and volumetric similarity = 0.867 using 6-fold Cross Validation (CV)), and also on in vivo T1-weighted MRI scans at typical resolutions (~1 mm isotropic). We also demonstrated that the method is robust in a test-retest setting and when applied to multimodal imaging (T2-weighted, Proton Density and quantitative T1 scans). To the best of our knowledge this is the first accurate method for automatic ultra-high resolution claustrum segmentation, which is robust against changes in contrast and resolution. The method is released at https://github.com/chiara-mauri/claustrum_segmentation and as part of the neuroimaging package Freesurfer (Fischl, 2012). |
| title | A Contrast-Agnostic Method for Ultra-High Resolution Claustrum Segmentation |
| topic | Computer Vision and Pattern Recognition Machine Learning Image and Video Processing |
| url | https://arxiv.org/abs/2411.15388 |