k-strip: A novel segmentation algorithm in k-space for the application of skull stripping

Objectives: Present a novel deep learning-based skull stripping algorithm for magnetic resonance imaging (MRI) that works directly in the information rich k-space. Materials and Methods: Using two datasets from different institutions with a total of 36,900 MRI slices, we trained a deep learning-base...

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Bibliographic Details
Published in:arXiv.org 2023-07
Main Authors: Rempe, Moritz, Mentzel, Florian, Pomykala, Kelsey L, Haubold, Johannes, Nensa, Felix, Kröninger, Kevin, Egger, Jan, Kleesiek, Jens
Format: Article
Language:English
Subjects:
Algorithms
Datasets
Deep learning
Image analysis
Image segmentation
Machine learning
Magnetic resonance imaging
Medical imaging
Skull
Strip
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Summary:Objectives: Present a novel deep learning-based skull stripping algorithm for magnetic resonance imaging (MRI) that works directly in the information rich k-space. Materials and Methods: Using two datasets from different institutions with a total of 36,900 MRI slices, we trained a deep learning-based model to work directly with the complex raw k-space data. Skull stripping performed by HD-BET (Brain Extraction Tool) in the image domain were used as the ground truth. Results: Both datasets were very similar to the ground truth (DICE scores of 92\%-98\% and Hausdorff distances of under 5.5 mm). Results on slices above the eye-region reach DICE scores of up to 99\%, while the accuracy drops in regions around the eyes and below, with partially blurred output. The output of k-strip often smoothed edges at the demarcation to the skull. Binary masks are created with an appropriate threshold. Conclusion: With this proof-of-concept study, we were able to show the feasibility of working in the k-space frequency domain, preserving phase information, with consistent results. Future research should be dedicated to discovering additional ways the k-space can be used for innovative image analysis and further workflows.
ISSN:2331-8422