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As I remember, yeah. 
They are two different paths. Build your version of the software or download and save the image in the SD.
I followed the steps in this guide (GitHub - googlecreativelab/open-nsynth-super: Open NSynth Super is an experimental physical interface for the NSynth algorithm). Regarding software, it only indicates:
- record the image on the SD
- run the script for the controller.
If the error is when running the script for the microcontroller, paste the code and the error here. I keep an eye on it.