Intratumour heterogeneity poses a challenge for the stratification of patients with glioblastoma (GBM). MRI, which is commonly used for diagnosis and assessment of response to treatment, was explored as a non-invasive tool to subclassify risk groups. Three clusters were identified: pre-multifocal, spherical and rim-enhancing. Each cluster was associated with a distinct molecular signature. Significant differences were detected in survival probability for each cluster; having pre-multifocal GBM was associated with the poorest survival rate, whereas patients with rim-enhancing GBM had the best survival rate. These results indicate that MRI can be used as a non-invasive tool to stratify patients with GBM to different treatment options.