A method for attenuation and scatter correction of brain single photon emission computed tomography (SPECT) is described where computed tomography (CT) images of the brain are used for the calculation of attenuation maps. The method is evaluated for the substance 99mTc hexamethylpropylene amine oxime. A transmission dependent scatter correction is utilized and is based on ray sums calculated through the attenuation map. A method based on external markers is used to align the SPECT and CT image volumes. The markers need only to be present during the SPECT acquisition since the corresponding landmarks can be found without markers on the CT images. The mismatching has been investigated for five patients who have undergone both a CT examination and a SPECT examination with markers. Twelve individuals from the staff have pointed out the landmarks on the CT images, with an average standard deviation of 3.4 mm. Reconstructions with an attenuation map shifted the corresponding 95% confidence interval have been performed to obtain an estimation of the quantitative uncertainty caused by the mismatching, and quantitative errors of up to 6.3% have been measured. At present the method is probably most useful when groups of patients are studied.