A system is provided for quantification of medical image data. First image obtaining means (1) are for obtaining a first image (A). Second image obtaining means (2) are for obtaining a second image (B). Spatial transformation obtaining means (3) are for obtaining spatial transformation information representing a correspondence between points in the first image and corresponding points in the second image. Identifying means (4) are for identifying a first image region (C) in the first image (A). Transforming means (5) are for transforming the first image region (C) into a corresponding second image region (C') in the second image (B) based on the spatial transformation information. Quantification means (6) are for computing a quantification relating to the second image region (C') by accessing image values of the second image (B) within the second image region (C').