Continual pretraining Prostate MRI ViT Encoder for task alignment

Building foundation models for MRI has emerged as a promising direction for advancing medical image analysis and improving accessibility of task specific models. Existing approaches primarily focus on effective pretraining strategies and evaluating their performance across diverse downstream tasks. While these methods show performance gains, limited attention has been given to understanding task alignment between pretraining and downstream objectives. Unlike language models, where the two stages are naturally aligned, such alignment is less evident in vision based applications. Motivated by this gap, we explore continual pretraining. Specifically, continually pretraining a pretrained ViT encoder using Low-Rank Adaptation (LoRA) on a prostate segmentation task to enhance task alignment and downstream performance. We further perform layer-wise representational analysis using Centered Kernel Alignment (CKA) to assess representational shifts and their correlation with task outcomes. Our experiments show improved performance in 3 of 6 downstream tasks and comparable results in the others. Our Feature analysis reveals that, for segmentation tasks, continually pretrained encoder features exhibit greater similarity to those of the finetuned encoder than the original pretrained encoder, correlating with observed performance gains.