In standard radiomics studies the features extracted from clinical images are mostly quantified with simple statistics such as the average or variance per Region of Interest (ROI). Such approaches may smooth out any intra-region heterogeneity and thus hide some tumor aggressiveness that may hamper predictions. In this paper we study the importance of feature aggregation within the standard radiomics workflow, which allows to take into account intra-region variations. Feature aggregation methods transform a collection of voxel values from feature response maps (over a ROI) into one or several scalar values that are usable for statistical or machine learning algorithms. This important step has been little investigated within the radiomics workflows, so far. In this paper, we compare several aggregation methods with standard radiomics approaches in order to assess the improvements in prediction capabilities. We evaluate the performance using an aggregation function based on Bags of Visual Words (BoVW), which allows for the preservation of piece-wise homogeneous information within heterogeneous regions and compared with standard methods. The different models are compared on a cohort of 214 head and neck cancer patients coming from 4 medical centers. Radiomics features were extracted from manually delineated tumors in clinical PET-FDG and CT images were analyzed. We compared the performance of standard radiomics models, the volume of the ROI alone and the BoVW model for survival analysis. The average concordance index was estimated with a five fold cross-validation. The performance was significantly better using the BoVW model 0.627 (95% CI: 0.616–0.637) as compared to standard radiomics0.505 (95% CI: 0.499–0.511), mean-var. 0.543 (95% CI: 0.536–0.549), mean0.547 (95% CI: 0.541–0.554), var.0.530 (95% CI: 0.524–0.536) or volume 0.577 (95% CI: 0.571–0.582). We conclude that classical aggregation methods are not optimal in case of heterogeneous tumors. We also showed that the BoVW model is a better alternative to extract consistent features in the presence of lesions composed of heterogeneous tissue.