Registering brain magnetic resonance imaging (MRI) scans containing pathologies is challenging primarily due to large deformations caused by the pathologies, leading to missing correspondences between scans. However, the registration task is important and directly related to personalized medicine, as registering between baseline pre-operative and post-recurrence scans may allow the evaluation of tumor infiltration and recurrence. While many registration methods exist, most of them do not specifically account for pathologies. Here, we propose a framework for the registration of longitudinal image-pairs of individual patients diagnosed with glioblastoma. Specifically, we present a combined image registration/reconstruction approach, which makes use of a patient-specific principal component analysis (PCA) model of image appearance to register baseline pre-operative and post-recurrence brain tumor scans. Our approach uses the postrecurrence scan to construct a patient-specific model, which then guides the registration of the preoperative scan. Quantitative and qualitative evaluations of our framework on 10 patient imagepairs indicate that it provides excellent registration performance without requiring (1) any human intervention or (2) prior knowledge of tumor location, growth or appearance.