Functional MRI (fMRI) is recognized as a well-established non-invasive diagnostic method to image activating cortical areas. Currently, the blood oxygenation level dependent (BOLD) contrast method is widely used in fMRI BOLD-fMRI images activating areas by detecting a reduced concentration of deoxyhemoglobin during neuronal activity, which is caused by a larger increase in O2 delivery compared with O2 consumption in normal adults. In the present study, near infrared spectroscopy, which is an optical method to evaluate cerebral blood oxygenation changes, has demonstrated an increase of deoxyhemoglobin associated with increases of oxyhemoglobin and total hemoglobin at activation areas of stroke patients, whereas BOLD-fMRI failed to image the activation areas. The present findings have serious applications for the application of BOLD-fMRI to the patients with brain disorders because BOLD-fMRI may overlook neuronal activities in these patients unless both increases and decreases of signals are considered.