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If the brain structural coordinates could be estimated using the individual head shape, magnetoencephalography and near-infrared spectroscopy would be more ideal brain functional imaging methods especially for young human children. First, we propose an algorithm to estimate brain coordinates with reference to the head surface shape in preschool children. Second, we examined its spatial error range using a leave-one-out procedure within 38 samples of child head and brain structures. The mean error of landmarks was 13.6±5.3 mm on the head surface and 18.5±12.4 mm in the intracranial structure between estimated and actual brain coordinates.