Parameter-Efficient pretrained-CT-to-MRI Transfer for Rectal Cancer Segmentation: Performance-Calibration Trade-offs

Although self-supervised pretraining is expected to learn broadly transferable representations, its effectiveness across imaging modalities substantially different from the pretraining domain, and on complex tumor-segmentation tasks, remains understudied. Evaluating CT-pretrained transformers on MRI rectal cancer segmentation, we identified two interacting failure modes in CT-to-MRI transfer: (a) inefficient token usage caused by zero-padding to match pretrained input dimensions, and (b) ineffective feature adaptation. We investigated these vulnerabilities using two primary CT-pretrained hierarchical shifted-window transformer backbones, SMIT and Swin UNETR, together with VoCo as a large-scale-pretrained supporting benchmark; these models differ in pretraining objectives and datasets. Mechanistic analysis leveraged an attention dilution index (ADI), an entropy-based metric quantifying attention diverted toward uninformative padding tokens, and centered kernel alignment (CKA) to measure feature reuse during MRI adaptation. ADI increased with zero-padding, while high feature reuse did not necessarily translate to improved downstream accuracy. To mitigate these issues, we introduced two interventions: a tumor-aware augmentation strategy to expand tumor appearance heterogeneity coverage, and an anisotropic cropping strategy to restore token efficiency. Fine-tuning with these strategies on identical rectal MRI datasets yielded detection rates of 91.1% (225/247) and 88.7% (219/247) for the primary SMIT and Swin UNETR backbones, with the supporting VoCo benchmark reaching 90.3% (223/247), demonstrating significantly improved robustness under CT-to-MRI transfer. This study is among the first to examine when pretrained transformers fail to transfer across imaging modalities and demonstrates how targeted mitigation strategies can systematically overcome cross-modality transfer limitations.

We evaluated parameter-efficient fine-tuning (PEFT) of the Segment Anything Model (SAM) for liver tumor segmentation in abdominal CT of colorectal liver metastases. We compared Low-Rank Adaptation (LoRA), 4-bit Quantized LoRA (QLoRA), a convolutional adapter (Conv-Adapter), and our Directional Spectral Top-K adapter (DiSCo), training only adapters while freezing the SAM backbone. DiSCo derives spectral bases from singular value decomposition of row-normalized weights and learns rank-gated spectral coefficients, per-output magnitude offsets, and a spectral gain, with optional Top-K rank selection at inference and 0.14 M trainable parameters. We benchmarked five prompting regimes: no prompt, single-point, multi-point, and bounding boxes at intersection over union 0.50 and 0.75. Conv-Adapter and LoRA achieved the highest accuracy (overall Dice 0.793 and 0.792; single-point Dice 0.795 and 0.792; 95th-percentile Hausdorff distance (HD95) 32 mm). QLoRA was close (overall Dice 0.766; single-point Dice 0.768; HD95 36.41 mm), with 0.91 M trainable parameters, 120 ms latency, and 4.9 GB peak memory. DiSCo achieved the highest Dice per million trainable parameters (4.66), with overall Dice 0.653, single-point Dice 0.698, and HD95 49.53 mm. These results show an accuracy-efficiency trade-off and support PEFT for liver tumor segmentation with reduced adaptation costs when compute and labeled data are limited. Code: https://github.com/Ramtin-Mojtahedi/PEFT-SAM-Liver-CT

Methods: Nine SSL methods spanning four pretext-task families were pretrained from scratch using the same 10{,}412 3D CT scans (1.89~M 2D axial slices) covering varied disease sites. The pretrained Swin Transformer encoder from each method was integrated into a SwinUNETR-style segmentation network (Swin encoder with a 3D CNN decoder and skip connections) and fine-tuned on nine public segmentation tasks of varying complexity, including large abdominal organs, head-and-neck structures, and tumors from CT and MRI. Performance was assessed using Dice similarity coefficient (DSC). Fine-tuning convergence speed, transferability across modalities (CT-to-MRI), and feature-reuse patterns between few- and many-shot fine tuning were further analyzed using centered kernel alignment. Results: Self-distilled masked image transformer (SMIT), which combines masked image modeling (MIM) with local and global self-distillation, achieved the highest overall segmentation accuracy across the nine tasks, the fastest fine-tuning convergence, and the smallest few-shot-to-many-shot performance gap, indicating the strongest data efficiency. SMIT also showed the most consistent feature-reuse patterns between few- and many-shot fine tuning. MIM-based SimMIM and self-distillation methods (DINO, iBOT) outperformed contrastive learning and rotation prediction, which rely on image-level global representations. Differences between SSL methods were largest in the few-shot setting and narrowed as the size of the labeled fine-tuning dataset increased, indicating that the choice of SSL pretraining matters most under limited annotation budgets.