Zero-Shot Vertebral Instance Segmentation on DICOM Spine Radiographs Using Promptable Segment Anything Models

TL;DR

This paper shows that AI models can accurately identify individual vertebrae in spine X-rays without prior training on such data, using rectangle prompts for better results.

Contribution

The study demonstrates the feasibility of zero-shot vertebral instance segmentation on raw DICOM spine radiographs using promptable foundation models.

Findings

SAM-ViT-Huge with rectangle prompting achieved the highest performance (mean IoU/Dice of 0.782/0.870 under oracle selection).

Rectangle prompting outperformed point prompting significantly in vertebral segmentation accuracy.

MedSAM-ViT-Base showed lower performance compared to SAM-based models, especially under model-score selection.

Abstract

Background: Accurate vertebral instance segmentation on full-spine radiographs is essential for spinal parameter assessment, but supervised methods require costly instance-level annotations and may be sensitive to domain shift. Methods: We investigated whether promptable segmentation foundation models can generalize zero-shot to raw DICOM spine radiographs without task-specific training. We evaluated SAM-ViT-Huge, SAM2-Hiera-Large, and MedSAM-ViT-Base on 144 full-spine radiographs with 1309 annotated vertebral masks using a standardized pipeline for DICOM decoding, intensity normalization, automatic prompt generation, and instance-level evaluation. For each prompt, models produced three candidate masks. Performance was reported under an oracle protocol selecting the candidate with the highest IoU against ground truth and a model-score protocol selecting the candidate with the highest predicted IoU. Metrics included IoU, Dice, precision, recall, ASSD, and HD95. Results: The best configuration was SAM-ViT-Huge with rectangle prompting, reaching a mean IoU/Dice of 0.782/0.870 under oracle selection and 0.737/0.837 under model-score selection. SAM2-Hiera-Large with rectangle prompting followed (0.744/0.848 oracle; 0.699/0.815 model-score), ahead of MedSAM-ViT-Base (0.599/0.737 oracle; 0.387/0.499 model-score). Point prompting yielded consistently low overlap (IoU 0.224–0.319; Dice 0.276–0.414) despite high recall, indicating systematic over-segmentation and large boundary errors. Conclusions: Zero-shot vertebral instance segmentation on raw DICOM spine radiographs is feasible with promptable foundation models when prompts sufficiently constrain target extent. Rectangle prompting is clearly more effective than point prompting in this setting.

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