Cardiovascular magnetic resonance has been shown to provide high data quality for myocardial perfusion assessment. However, to analyze the perfusion data, some signal processing and modeling is needed to correct for motion related artifacts and limited spatial resolution. This study describes a method based on system identification, allowing, after a first step of image registration, to integrate and correct the partial volume effect in the myocardium perfusion quantification. This method is then applied to patients with coronary artery disease or hypertrophic obstructive cardiomyopathy.