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As far as I know, CTs can't detect brain tumors, which can cause headaches, which is why they want you to get an MRI.
I didn't get bruising from Indocin when I took it

I had three CT with my first CH nothing my first MRI found my pituitary  tumor (pituitary tumors most all for the most part are benign) good news, was no headaches for four years after tumor removal, bad news, chronic cluster headaches for three after, which is where I am to date, lots of info online about pituitary surgery and CH, Good news new research , on my second week of new found drug Octreotide, and now starting D3 therapy. Have had another CT and two more MRI with and without contrast since 2009 no new tumor . Good luck do your homework, 

An MRI found my benign pineal cyst, if I recall. Most recently, I was scanned because of head trauma. There are all types of MRI machines from ones that only enclose the extremity to ones that are closed (tunnels). If you are anxious, let them know. You can be sedated if necessary. Also let them know if you have any implants.

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