With the use of functional MRI (fMRI), we studied the changes in brain hemodynamic activity of healthy subjects during motor imagery training with the use brain-computer interface (BCI), which is based on the recognition of EEG patterns of imagined movements. ANOVA dispersion analysis showed there are 14 areas of the brain where statistically sgnificant changes were registered. Detailed analysis of the activity in these areas before and after training (Student's and Mann-Whitney tests) reduced the amount of areas with significantly changed activity to five; these are Brodmann areas 44 and 45, insula, middle frontal gyrus, and anterior cingulate gyrus. We suggest that these changes are caused by the formation of memory traces of those brain activity patterns which are most accurately recognized by BCI classifiers as correspondent with limb movements. We also observed a tendency of increase in the activity of motor imagery after training. The hemodynamic activity in all these 14 areas during real movements was either approximatly the same or significantly higher than during motor imagery; activity during imagined leg movements was higher that that during imagined arm movements, except for the areas of representation of arms.