In my previous employment, two women had allowance for "intermittant FMLA" for migraines.  They were able to take off a day or two here and there as needed.  Don't know more than that about it though.

I sure have... it really doesn't matter a whole lot what your HR department thinks.  It matters what your doctor thinks.   You can decide with your doctor how you want to approach it (intermittent, short term, specific dates, long term, etc.) depending on how you cycle and treat.   Intermittent FMLA would likely be the best fit though.  

You request the paperwork from your company and bring it to your doctor.  Your doctor will fill it out and specify how long each incedent can last (I would suggest something like a range of 3 hrs to 1 day to cover you if you need to miss part of a day or a whole day) and number of incedents (I would again suggest a range of 15-20/mo to allow a bad cycle to be covered for a lot of incidents).  Get it all filled out and submit it to HR for approval.  If HR denies your FMLA claim they will need to explain why and how it is legal for them to deny it. This is extremely unlikely if your dcotor did everything right, and if it isn't filled out/submitted correctly you'll have a chance to correct it.  

Once it's approved you can use it.  Each company is different in how they'll want you to track your FMLA use and how you need to notify them or activate the FMLA ttime.  Likely you'll need to request off specifying that it is FMLA coverage, and then  upon returning to work document your abscence with a FMLA form within a specified time frame.   This document, or a document with a collection of incidents would then be sent to HR daily, weekly,bi-weekly, monthly, etc... whatever they do at your company. 

You can use the FMLA this way up to you doctors limits and within the alotted annual usage guidelines for both federal FMLA guidelines and those of your specific State.  This means if your doctor says your incident can be up to 1 day for up to 20 incidents per month, and there are 21 work days in a month, and you missed all or or part of a  work day 20 times in the month due to CH, that last day wont be covered.  It also means that come the next month you'll have 20 more incidents available up to the max amount total for the year.  Some states give you days in addition to the Federal guidelines, so check into that as well if need be.  

In Wisconsin there are less days allowed than by Federal standards, but they reset annually on January 1st whereas the Federal days are on a rolling calendar.  So I'd exhaust my State days before I use up all of the Federal days as they're counted concurrently.  However, If I started using up FMLA days in July, ran out of my Federal days by December, the State days would reset on 1/1 giving me those extra days for the following year even though Im out of Federal days until the following July.  This, of course, could be different where you live.

Thanks for the great info Slhass!  I greatly appreciate it.