GOUHFI: a novel contrast- and resolution-agnostic segmentation tool for Ultra-High Field MRI
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| Main Authors: | , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866911184729407488 |
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| author | Fortin, Marc-Antoine Kristoffersen, Anne Louise Larsen, Michael Staff Lamalle, Laurent Stirnberg, Ruediger Goa, Paal Erik |
| author_facet | Fortin, Marc-Antoine Kristoffersen, Anne Louise Larsen, Michael Staff Lamalle, Laurent Stirnberg, Ruediger Goa, Paal Erik |
| contents | Recently, Ultra-High Field MRI (UHF-MRI) has become more available and one of the best tools to study the brain. One common step in quantitative neuroimaging is to segment the brain into several regions, which has been done using software packages like FreeSurfer , FastSurferVINN or SynthSeg. However, the differences between UHF-MRI and 1.5T or 3T images are such that the automatic segmentation techniques optimized at these field strengths usually produce unsatisfactory segmentation results for UHF images. Thus, it has been particularly challenging to perform region-based quantitative analyses as typically done with 1.5-3T data, underscoring the crucial need for developing new automatic segmentation techniques designed to handle UHF images. Hence, we propose a novel Deep Learning (DL)-based segmentation technique called GOUHFI: Generalized and Optimized segmentation tool for Ultra-High Field Images, designed to segment UHF images of various contrasts and resolutions. For training, we used a total of 206 label maps from datasets acquired at 3T, 7T and 9.4T. In contrast to most DL strategies, we used a domain randomization approach, where synthetic images were used to train a 3D U-Net. GOUHFI was tested on seven different datasets and compared to existing techniques like FastSurferVINN,SynthSeg and CEREBRUM-7T. GOUHFI was able to segment the six contrasts and seven resolutions tested at 3T, 7T and 9.4T. Average Dice scores of 0.90, 0.90 and 0.93 were computed against the ground truth segmentations at 3T, 7T and 9.4T, respectively. Ultimately, GOUHFI is a promising new segmentation tool, being the first of its kind proposing a contrast- and resolution-agnostic alternative for UHF-MRI without requiring fine-tuning or retraining, making it the forthcoming alternative for neuroscientists working with UHF-MRI or even lower field strengths. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2505_11445 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | GOUHFI: a novel contrast- and resolution-agnostic segmentation tool for Ultra-High Field MRI Fortin, Marc-Antoine Kristoffersen, Anne Louise Larsen, Michael Staff Lamalle, Laurent Stirnberg, Ruediger Goa, Paal Erik Image and Video Processing Recently, Ultra-High Field MRI (UHF-MRI) has become more available and one of the best tools to study the brain. One common step in quantitative neuroimaging is to segment the brain into several regions, which has been done using software packages like FreeSurfer , FastSurferVINN or SynthSeg. However, the differences between UHF-MRI and 1.5T or 3T images are such that the automatic segmentation techniques optimized at these field strengths usually produce unsatisfactory segmentation results for UHF images. Thus, it has been particularly challenging to perform region-based quantitative analyses as typically done with 1.5-3T data, underscoring the crucial need for developing new automatic segmentation techniques designed to handle UHF images. Hence, we propose a novel Deep Learning (DL)-based segmentation technique called GOUHFI: Generalized and Optimized segmentation tool for Ultra-High Field Images, designed to segment UHF images of various contrasts and resolutions. For training, we used a total of 206 label maps from datasets acquired at 3T, 7T and 9.4T. In contrast to most DL strategies, we used a domain randomization approach, where synthetic images were used to train a 3D U-Net. GOUHFI was tested on seven different datasets and compared to existing techniques like FastSurferVINN,SynthSeg and CEREBRUM-7T. GOUHFI was able to segment the six contrasts and seven resolutions tested at 3T, 7T and 9.4T. Average Dice scores of 0.90, 0.90 and 0.93 were computed against the ground truth segmentations at 3T, 7T and 9.4T, respectively. Ultimately, GOUHFI is a promising new segmentation tool, being the first of its kind proposing a contrast- and resolution-agnostic alternative for UHF-MRI without requiring fine-tuning or retraining, making it the forthcoming alternative for neuroscientists working with UHF-MRI or even lower field strengths. |
| title | GOUHFI: a novel contrast- and resolution-agnostic segmentation tool for Ultra-High Field MRI |
| topic | Image and Video Processing |
| url | https://arxiv.org/abs/2505.11445 |