Actually, migraines should NOT be causing this much pain, migraine attacks should not occur on a daily basis and if they occur on a daily basis then they do require serious interventions. FIrt of all, we need to confirm that this is truly migraine and not anything else, it needs to be confirmed that the cyst is not causing him these headaches. While it is not likely that a cyst of this size would be responsible for these headaches it is certainly possible especially if the headaches are localized to that region of the head. If the cyst is found to be responsible for the pain then it should be managed with drainage. Your neurologist should be able to confirm this by examining him thoroughly and possibly even repeating the MRI scan if it was done more than 6 months ago.
Now if migraines are found to be the cause then his medications need to be changed, the medications which he is on currently are used to prevent attacks of a migraine however they clearly don't seem to be working. Usually, preventive medications are successful limiting the attacks to once or twice a month but here he is in constant pain which is not right. Basically, he should have medications like sumatriptan or zolmitriptan to abort acute attacks on hand or even simple medications like ibuprofen or naproxen along with a muscle relaxant like tizanidine (movax) which would provide immediate relief. In addition the dose of topagen should be increased to 100 mg a day if 50 mg is not working to control the attacks however there are other options which can be tried which include,
Calcium channel blockers
If those do not work then in refractory cases we can inject botox into his scalp muscles which can help manage the severest forms of migraines. My suggestion is to visit his neurologist once again and have him change the medications or discuss getting botox for him, botox injections do work well in teenagers. Additionally, I have found that amitriptyline seems to work well in male teenagers of his age group so it would be worthwhile to try using that drug here.
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