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In a two-hour meeting, Ms Siddiqui informed the consul general that she was medically fine and was pleased to speak by phone to her mother and children in Karachi on Thursday.
According to a Pakistani embassy official, Dr Aafia Siddiqui will also be able to meet her brother at her request.
The consul general informed Ms Siddiqui that the Pakistani embassy in Washington had coordinated consular access for her through the concerned authorities.
Dr Siddiqui asked the diplomat to convey her thanks to Ambassador Haqqani for his concern for her welfare, the official said.