Deficits have continued to plague the MBTA. Going into November, the transit agency was about $25 million in the hole, despite receiving $160 million in sales tax revenues for fiscal 2010. But help was on the way.

How did the transit agency get most of that FY 2010 red ink off the books?

Paging Uncle Sam. Last week, the Boston Region Metropolitan Planning Organization (MPO) dedicated about $18 million in federal economic stimulus funds to the MBTA for system-wide operating assistance.

The MPO’s Transportation Improvement Program (TIP) list determines which transportation projects can receive stimulus funds. In addition, under the provisions of the American Recovery and Reinvestment Act, the MPO can authorize transit agencies to use a small percentage of stimulus funds for operating expenses — and the MPO went for the maximum amount allowable.

There are still red splotches on the MBTA’s ledger; but the agency can manage a single-digit deficit, according to Eric Bourassa, the Metropolitan Area Planning Council’s transportation manager. (MAPC sits on the planning organization’s board and helps decide which TIP projects receive federal funds.)

Two other transit authorities in the Boston Region MPO also received federal dollars to help close budget gaps: the Metro West RTA received $75,000 and the Cape Ann Transit Authority nearly $68,000.Â