Automated Detection of Multiple Sclerosis Lesions on 7-tesla MRI Using U-net and Transformer-based Segmentation

Background: The lateral ventricle choroid plexus (LVCP) is gaining recognition as a key imaging biomarker for multiple sclerosis (MS) related to physical disability and neuroinflammation. Yet, manual segmentation of the LVCP is highly tedious, restricting its use in broad clinical trials and longitudinal assessments. This research aims to develop a SwinUNETR-driven pipeline that leverages targeted intra- and peri-ventricular small patch sampling to automatically segment the LVCP in MS from both standalone and multi-modal MRI inputs. Methods: We retrospectively assessed 3T MRI scans across three sets of data stemming from two separate MS-dominant cohorts (Dataset 1: n=177; Dataset 2: n=177; expanded test set: n=388). Our method employed a SwinUNETR architecture trained on 32x32x32 voxel patches, benchmarking it against the 3D UXNET model. The primary metric for evaluation was the Dice Similarity Coefficient (DSC), supplemented by computational demand (GFLOPs) and the 95th percentile Hausdorff Distance (HD95). Results: On the extended test set, the SwinUNETR model secured a mean DSC of 0.868 (95% CI: 0.863-0.872) with MPRAGE and FLAIR combined, showing a statistically significant gain over UXNET (DSC: 0.858 [95% CI: 0.853-0.862], p<0.0001). When restricted to standalone FLAIR inputs, the transformer-based approach sustained a high DSC of 0.863, while the spatial localization of UXNET worsened considerably (HD95: 1.86 vs. 3.00 mm). Importantly, the proposed framework lowered computational load by 99% (91.8 vs. 22,080 GFLOPs). By integrating localized patch sampling with a SwinUNETR architecture, this methodology offers an accurate, robust, and statistically superior alternative to current leading models for LVCP segmentation. Its vast reduction in computational cost makes it ideal for widespread implementation in clinical and research environments.

Ultra-high resolution 7 tesla (7T) magnetic resonance imaging (MRI) provides detailed anatomical views, offering better signal-to-noise ratio, resolution and tissue contrast than 3T MRI, though at the cost of accessibility. We present an advanced deep learning model for synthesizing 7T brain MRI from 3T brain MRI. Paired 7T and 3T T1-weighted images were acquired from 172 participants (124 cognitively unimpaired, 48 impaired) from the Swedish BioFINDER-2 study. To synthesize 7T MRI from 3T images, we trained two models: a specialized U-Net, and a U-Net integrated with a generative adversarial network (GAN U-Net). Our models outperformed two previous state-of-the-art 3T-to-7T models in image-based evaluation metrics. Four blinded MRI professionals judged our synthetic 7T images as comparable in detail to real 7T images, and superior in subjective visual quality to 7T images, due to the reduction of artifacts. Using both SynthSeg and NextBrain, automated segmentations of the synthetic 7T images were more similar to real 7T segmentations than automated segmentations from the 3T images that were used to synthesize the 7T images. Finally, synthetic 7T images showed similar performance to real 3T images in downstream prediction of cognitive status using MRI derivatives (n=3,168). In all, we show that synthetic T1-weighted brain images approaching 7T quality can be generated from 3T images, which may improve image quality and segmentation, without compromising performance in downstream tasks. Future directions, possible clinical use cases, and limitations are discussed.

Small lesions in brain MRI are hard to segment because they occupy a tiny fraction of the volume and are dominated by background and larger lesions during voxel-wise optimization, so a model can reach a high Dice similarity coefficient (DSC) while missing many of them. We propose CATMIL, a training objective that adds two auxiliary terms to the standard nnU-Net Dice and cross-entropy loss without changing the architecture. The Component-Adaptive Tversky (CAT) term weights lesion voxels by the inverse size of their connected component, so each lesion contributes nearly equally regardless of volume. The lesion-level Multiple Instance Learning (MIL) term treats each lesion as a bag of voxels and penalizes lesions with no detected voxel. For multiple sclerosis lesion segmentation on MSLesSeg, CATMIL achieves the highest small-lesion recall (0.873 vs. 0.796 for Dice+CE; 95% CI of the difference +0.030 to +0.157, higher in all six test patients) and about 48% fewer missed lesions, with comparable DSC and HD95. The gain holds for lesions of at least 3 mm in diameter, the clinical reading size (recall 0.944 vs. 0.870). Standard losses produce no probability response to most small lesions they miss, so no threshold can recover them. The cost is more small false-positive components; a simple component-size filter removes most of them while keeping the sensitivity gain, and at matched lesion-wise precision CATMIL detects more small lesions with higher lesion-wise F1. An ablation attributes the detection gain to the MIL term. On a second dataset, 3D-MR-MS, CATMIL with the same loss weights again improves small-lesion recall, at a larger false-positive cost and slightly lower DSC. Code: https://github.com/luumsk/SmallLesionMRI