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

Abstract

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.

Type
Moritz Rempe
Moritz Rempe
Master Student
Jan Egger
Jan Egger
Team Lead AI-guided Therapies
Jens Kleesiek
Jens Kleesiek
Professor of Translational Image-guided Oncology