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I have a problem with my hardware for an experiment I am preparing to run. I have bought a pair of research grade etymotic earphones for circa £500. They end up in two 6.5mm jacks. I need to plug them into the 3.5mm headphone input on my MacBook Pro laptop using an adaptor.

I have modified the sounds (1000 sounds) in MatLab so that 500 sounds have reduced volume on the Right, and 500 reduced volume on the Left. I am studying the interaction between falling-asleep-to-losing-consciousness and various sounds being played on the left and on the right ear. When I play the sounds through my laptop's speakers, I can clearly hear the sounds coming from the left and the right speakers as they should. When I plug in the 6.5mm jacks to the macbook pro headphone through an 6.5 to 3.5mm adapter and I hear the sound via the headphone, the separation between the left and the right volume modifications is lost.

Its a big issue and has stopped my research dead. I am not sure how to proceed.

Any ideas please?

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You have the wrong adapter. You have a signal splitter rather an a dual mono to stereo converter. 3.5mm and 6.5mm jacks have multiple possible configurations of the connector. The most common are TS (tip/sleeve), TRS (tip/ring/sleeve) and TRRS (tip/ring/ring/sleeve). Each of these serves a different purpose.

In all cases, one portion is the ground, the remaining portions are for different signals. In the case of TS, or a mono cable, there is only one channel of audio. If you insert a TS cable in to a jack for TRS or TRRS, the rings will also make contact with the sleeve. TRS can be used for either stereo (with two signals as you are doing) or for balanced audio (mono audio where the noise is flipped in phase and canceled out). TRRS is most typically used for things like headsets where you have stereo audio and also have a microphone input.

The cable you currently have is only designed to work with TS cables. It takes the sleeve and connects it to both sleeves and takes the tip and connects it to both tips, so you get the same signal to both earphones. It may also be a stereo splitter where the ring is involved but is just duplicated to each as well.

What you need is a stereo to dual mono adapter or a TRS to dual TS adapter. This will have a TRS plug and two TS sockets which will wire one tip to the tip and the other tip to the sleeve of the TRS connector. This will accomplish what you are looking for and should have one plug marked as L and one plug marked as R. You can alternately find it as an "insert" cable, though it will be labeled in/out (or tip and ring) rather than R/L. Insert cables are also likely to have male ends rather than female ends, so you'll need barrel connectors if you use one. Insert cables are used with professional sound boards to output a signal for external processing and then take the result of the processing back in via the same connector, but they have the same wiring as the cable you need.

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