Federal investigators with the NTSB were reviewing the crash that also injured 15 people.
The MTA said they will start a pilot program to test for sleep apnea after the NTSB recommendations.
The agency has developed new systems for training workers, inspecting tracks and reducing train speeds.
The broken rail was found Tuesday along the F line during a routine inspection north of 36th Street.
Four injured people were taken to hospitals while local service was restored for evening rush, MTA said.
Metro-North must formulate a plan by Dec. 31 for signal modifications to ensure safety.
The MTA planned to provide near full service on the Hudson Line, with scattered delays.
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