arXiv subjects

Hendrik Kristian Möller

Publications and source records attributed to Hendrik Kristian Möller.

2 recordsLinked to original sources

arXiv2025

VIBESegmentator: Full Body MRI Segmentation for the NAKO and UK Biobank

Objectives: To present a publicly available deep learning-based torso segmentation model that provides comprehensive voxel-wise coverage, including delineations that extend to the boundaries of anatomical compartments. Materials and Methods: We extracted preliminary segmentations from TotalSegmentator, spine, and body composition models for Magnetic Resonance Tomography (MR) images, then improved them iteratively and retrained an nnUNet model. Using a random retrospective subset of German National Cohort (NAKO), UK Biobank, internal MR and Computed Tomography (CT) data (Training: 2897 series from 626 subjects, 290 female; mean age 53+-16; 3-fold-cross validation (20% hold-out). Internal testing 36 series from 12 subjects, 6 male; mean age 60+-11), we segmented 71 structures in torso MR and 72 in CT images: 20 organs, 10 muscles, 19 vessels, 16 bones, ribs in CT, intervertebral discs, spinal cord, spinal canal and body composition (subcutaneous fat, unclassified muscles and visceral fat). For external validation, we used existing automatic organ segmentations, independent ground truth segmentations on gradient echo images, and the Amos data. We used non-parametric bootstrapping for confidence intervals and Wilcoxon rank-sum test for computing statistical significance. Results: We achieved an average Dice score of 0.90+-0.06 on our internal gradient echo test set, which included 71 semantic segmentation labels. Our model ties with the best model on Amos with a Dice of 0,81+-0.14, while having a larger field of view and a considerably higher number structures included. Conclusion: Our work presents a publicly available full-torso segmentation model for MRI and CT images that classifies almost all subject voxels to date.

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arXiv2023

Denoising diffusion-based MRI to CT image translation enables automated spinal segmentation

Background: Automated segmentation of spinal MR images plays a vital role both scientifically and clinically. However, accurately delineating posterior spine structures presents challenges. Methods: This retrospective study, approved by the ethical committee, involved translating T1w and T2w MR image series into CT images in a total of n=263 pairs of CT/MR series. Landmark-based registration was performed to align image pairs. We compared 2D paired (Pix2Pix, denoising diffusion implicit models (DDIM) image mode, DDIM noise mode) and unpaired (contrastive unpaired translation, SynDiff) image-to-image translation using "peak signal to noise ratio" (PSNR) as quality measure. A publicly available segmentation network segmented the synthesized CT datasets, and Dice scores were evaluated on in-house test sets and the "MRSpineSeg Challenge" volumes. The 2D findings were extended to 3D Pix2Pix and DDIM. Results: 2D paired methods and SynDiff exhibited similar translation performance and Dice scores on paired data. DDIM image mode achieved the highest image quality. SynDiff, Pix2Pix, and DDIM image mode demonstrated similar Dice scores (0.77). For craniocaudal axis rotations, at least two landmarks per vertebra were required for registration. The 3D translation outperformed the 2D approach, resulting in improved Dice scores (0.80) and anatomically accurate segmentations in a higher resolution than the original MR image. Conclusion: Two landmarks per vertebra registration enabled paired image-to-image translation from MR to CT and outperformed all unpaired approaches. The 3D techniques provided anatomically correct segmentations, avoiding underprediction of small structures like the spinous process.

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