Region-based compression technique is particularly useful for radiological archiving system as it allows diagnostically important regions to be compressed with near lossless quality while the non-diagnostically important regions (NROI) to be compressed at lossy quality. In this paper, we present a region-based compression technique tailored for MRI brain scans. In the proposed technique termed as automated arbitrary PCA (AAPCA), an automatic segmentation based on brain symmetrical property is used to separate the ROI from the background. The arbitrary-shape ROI is then compressed by block-to-row PCA algorithm (BTRPCA) based on a factorization approach. The ROI is optimally compressed with lower compression rate while the NROI is compressed with higher compression rate. The proposed technique achieves satisfactory segmentation performance. The subjective and objective evaluation performed confirmed that the proposed technique achieves better performance metrics (PSNR and CoC) and higher overall compression rate. The experimental results also demonstrated that the proposed technique is more superior to various state-of-the-art compression methods.