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To record with the MicroTrack II's 1/4” inputs, you must record from a balanced source with TRS balanced cables. If you are recording from an unbalanced line level source or a microphone with an unbalanced (TS) cable, use the 1/8” input instead; connecting unbalanced cables to the 1/4" TRS inputs yields an audible clicking sound that is recorded. You can change your input source from the MicroTrack II’s Main Menu>Record Settings>Input Source.
If you are recording with a phantom powered condenser microphone, you must use a TRS balanced cable; please see this article.
If you are recording with an Audio Technica AT822 please see this article.
Note: When recording with only 1 balanced input, it is recommended to unlink the L/R gain controls (Menu>Record Settings>Link L+R Gain>Off) and turn the input gain for the unused input all the way down.