Hi Chiara, 

Sorry for replying so late. 

1) You are correct. I have to clarify there are two invert parameters in PANDA. One is in Diffusion Opt panel and the other should be in Deterministic fiber tracking options of Tracking Opt panel. If you find invert Z is correct, then you should set the invert parameter in the Tracking Opt panel to Invert Z, not the invert parameter in Diffusion Opt panel. 

You know the coordinates of different MRI scanners could be different with FSL and Diffusion Toolkit. So, the invert and swap of Diffusion Opt panel was used to change the coordinates of the diffusion images to be the same with FSL. And the invert and swap of Tracking Opt panel was used to change the coordinates of the diffusion images to be the same with Diffusion Toolkit (DTK), as DTK was used to do deterministic fiber tracking. 

Then, generally, for most data, you don't need to set the invert and swap in diffusion opt panel, as the coordinates of the most data were the same with FSL coordinates. And if your image was already with the same coordinates of FSL, then the change from FSL coordinate to DTK coordinate was fixed. it's Invert Z. Therefore, in the new version, I removed the invert and swap parameters of Tracking Opt panel, and set it as 'Invert Z' in the codes. 

So, in your case, just left it as the default parameters, and do not change invert or swap parameters. And finally, the images of the tractography should be the golden standard. Only one option will be right, and you will find it from the tractography image. 

2) About _S, PANDA's deterministic fiber tracking was based on Diffusion Toolkit, you may find more information from the website of DTK. _S means this image was smoothed version of the original tractography image. Generally, we use use the original one. 

Hope it is helpful.

Thank you.
Zaixu