During calibration of a SPECT system, system-specific sensitivities and cross-calibration factors for multiple isotopes for correcting for dose are determined for various combinations of options, including the option of which specific well counter with which to measure the dose. The options may include selected energy windows for isotopes with multiple energy windows. This arrangement allows for custom-specified isotopes not included in standard listings. For use with a particular patient, the cross-calibration factor for the well counter used to measure the dosage for the patient is accessed and used for dose correction. More accurate quantitative functional information may result from the corrected dose. The cross-calibration may be more easily implemented despite the options using the sensitivities and cross-calibrations provided for various combinations.