I am so sorry; I did not see this reply. Did you ever get PyDesigner working?

You have to make sure you have a conda environment set up and active before installing PyD. 

1. If you have that already, I would try to navigate into the directory where the raw data is and run it that way to see if it works.
   
2. Next, if that doesn't work, I'd try just giving pydesigner the dicom folder as the input since it can work with that, too. 
   

Also, FYI: if the data is partial Fourier, the Gibbs unringing will not run as it is currently only for full Fourier encoding. 

Again, I apologize for not responding quickly. If you could ask any other debug questions on the PyDesigner GitHub page, we monitor that regularly.

-Hunter