I try to use DSI model to do tractography. However, it seems that MRtrix3 does provide this method, so I turn to use DSI studio software to get the fiber track. And the output of DSI studio is in .trk format. Then I use the code provided by Marc Côté on Github to convert .trk to .tck. But the position of the fiber is wrong which is shown in figure below. Could you please give me any advice?
I think the trk format stores the positions of the streamline vertices relative to the image axes, whereas MRtrix3 assumes they’re stored in real/scanner coordinates. So the issue is likely related to providing the wrong image as reference to the converter – this is needed to work out the mapping between the coordinates in the two formats. I’ve no experience with actually using the converter myself, but hopefully that’ll be enough information for you to fix the problem…