Is it possible to measure cortisol levels specifically in the hypothalamic–pituitary–adrenal (HPA) axis in a living human? Or do cortisol blood tests just assume that increased cortisol means they may have an effect on this region?
One could measure these hormones in catheters placed in the carotid artery and jugular vein to have a good estimate of levels the brain is exposed to. It would be more challenging to measure levels to and from the adrenal gland without more invasive techniques. One could (should?) assume that the levels in the carotid artery primarily reflect the output from the adrenal gland. If you want a non-invasive approach, perhaps measuring levels in saliva would be useful.
Why not measure cortisol levels in correlation to another hormone specific to the HPA in which case you can show that the two are tied together that as one hormone from the HPA spikes, cortison is directly before or behind it showing possible causality or effect.