This paper presents a novel liver segmentation algorithm that achieves higher performance than conventional algorithms in the segmentation of cases with unusual liver shapes and/or large liver lesions. An L1 norm was introduced to the mean squared difference to find the most relevant cases with an input case from a training dataset. A patient-specific probabilistic atlas was generated from the retrieved cases to compensate for livers with unusual shapes, which accounts for liver shape more specifically than a conventional probabilistic atlas that is averaged over a number of training cases. To make the above process robust against large pathological lesions, we incorporated a novel term based on a set of “lesion bases” proposed in this study that account for the differences from normal liver parenchyma. Subsequently, the patient-specific probabilistic atlas was forwarded to a graph-cuts-based fine segmentation step, in which a penalty function was computed from the probabilistic atlas. A leave-one-out test using clinical abdominal CT volumes was conducted to validate the performance, and proved that the proposed segmentation algorithm with the proposed patient-specific atlas reinforced by the lesion bases outperformed the conventional algorithm with a statistically significant difference.