I am from India. I was on F1 OPT for the first 9 months in 2012 and H1B for the remaining. I am Single.

1) Where do I specify my Health Savings Account info for Tax exemption?
2) Where do I specify the tax exemption that I can avail via the Income Tax treaty that US has with India(I believe its 5900 this year)?
3) Can I still fill in 3800 the exemptions part of 1040-NR(Line40) while I avail the above bullets?

Thank you

1) Form 8889 is used to claim the HSA deduction.

2) For 2012, your claim the $5,950 standard deduction where the itemized deduction is normally (Line 38) and print "Standard deduction allowed per Article 21(2) of U.S.-India Tax Treaty" on the dotted line to the left of the $5,950 entry.

3) Yes, you still get your $3,800 personal exemption.

Please allow me to ask my question in this thread, as my situation is very similar to OP. A little background:

F-1 08/2009 to 08/2011
OPT 08/2011 to 10/2012
H-1 10/2012 to present.

How should I file? NR, R or dual? I see that the OP has been advised to file as a Non-resident if he claims standard deduction under treaty and personal allowance. Should I do the same?

How about FICA? Do I include them anywhere on the forms? Basically, I am confused how does FICA taxation for 3 months come into play while filing the return? Do I get any refund, partial refund for those three months if you suggest filing as NR? Or, Should I file multiple forms?

FICA (Social Security and Medicare) taxes are NOT addressed on the annual INCOME tax return. They are flat taxes withheld from your salary starting, for you, on 1 October 2012. If they were withheld before that, go tou your employer and ask for a refund.

If you are single, you should file as a non-resident, filing Forms 1040NR-EZ and 8843 one last time.

If you believe that you will need professional help filing this year, this IS what I do. Please double-click on my name (Atlanta Tax Expert) above to access my profile. You will find my email address in the signature portion of the profile (scroll down to the BOTTOM of the page).