In this work we present methods and algorithms for construction of a personalized model of coronary haemodynamics based on computed tomography images. This model provides estimations of fractional flow reserve, coronary flow reserve, and instantaneous wave-free ratio taking into account transmural perfusion ratio indices obtained from perfusion images. The presented pipeline consists of the following steps: aorta segmentation, left ventricle wall segmentation, coronary arteries segmentation, construction of 1D network of vessels, partitioning of left ventricle wall, and personalization of the model parameters. We focus on a new technique, which generates specific perfusion zones and computes transmural perfusion ratio according to the quality of available medical images with a limited number of visible terminal coronary vessels. Numerical experiments show that accurate evaluation of stenosis before precutaneous coronary intervention should take into account both fractional flow reserve indices and myocardial perfusion, as well as other indices, in order to avoid misdiagnosis. The presented model provides better understanding of the background of clinical recommendations for possible surgical treatment of a stenosed coronary artery.