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Objective To evaluate the changes in near infrared spectroscopy (NIRS) absorptive properties induced by cerebral ischemia.rnMethods A dual wavelength (760?nm and 850?nm) NIRS system measuring total hemoglobin concentration changes was constructed. Twenty Sprague-Dawley rats were used to set up middle cerebral artery occlusion (MCAO) model that had a stable ischemia focus on the cortex. We used NIRS to localize the ischemia focus that was confirmed with magnetic resonance imaging (MRI) and triphenyltetrazonlium chloride brain staining. The cortical ischemia area and the geometric configuration of the NIRS topograms were compared with those from MRI and the anatomical samples for the same rat.rnResults The reconstructed NIRS topograms showed that there was an optical density decreased area on the left cortex of the rats with MCAO model. The mean ischemia area as shown in NIRS images was 19.50?mm2 (19.50±0.35?mm2, n=20). Anatomical samples showed that the mean ischemic area located in the NIRS measurement area was 18.46?mm2 (18.46±0.38?mm2, n=20). For MRI, the mean ischemia area located in the NIRS measurement area was 20.71?mm2 (20.71±0.27?mm2, n=20). There were no significant differences among NIRS, MRI and anatomical samples (F(2,57)=2.47, P>0.05) for defining the ischemia area. The results showed that there was a significant correlation among NIRS, MRI (r=0.782, P<0.05) and anatomical sample (r=0.851, P<0.05) for the same cortical ischemia area. Meanwhile, the location and geometric configuration of the ischemia focus shown by NIRS were identified by MRI and anatomical samples, though the NIRS images had worse spatial resolution.rnConclusions NIRS showed a good agreement with MRI and anatomical samples in the ischemic area and location determination of the infarction focus for the rat MCAO model. The study suggests that NIRS can non-invasively trace cortical hemodynamic changes induced by ischemia in real time.