said the best way is to start with V/Q scan and ideally you have to be do a perfusion scan and if negative stop it. But if you use xenon for ventilation it should be administered before the perfusion. Most places use xenon because it is more cost-efficient.
CTA has one advantage and one disadvantage.
It is coned down on the mother's chest and the scattered dose to the fetus is less. On the other hand for V/Q scan the scattered dose to the baby is much higher. The expected dose to the fetus in a CT is less than 50 uSV. Also on the third trimester the baby is usually in the pelvis and many times the head is located inferiorly, so most of the dose to the fetus is to his buttocks.
On the other hand, for an optimal CTA for PE, the patient should be in expiratory phase. In pregnancy for many reasons it is more difficult to obtain and the false positives are higher.
There are a lot of controversy on this issue and it is institution by institution. At our facility we do CT.