A method and system for measuring the volume of the left ventricle (LV) in a 3D medical image, such as a CT, volume is disclosed. Heart chambers are segmented in the CT volume, including at least the LV endocardium and the LV epicardium. An optimal threshold value is automatically determined based on voxel intensities within the LV endocardium and voxel intensities between the LV endocardium and the LV epicardium. Voxels within the LV endocardium are labeled as blood pool voxels or papillary muscle voxels based on the optimal threshold value. The LV volume can be measured excluding the papillary muscles based on the number of blood pool voxels, and the LV volume can be measured including the papillary muscles based on the total number of voxels within the LV endocardium.