Incomplete Fibres

Are you referring to this post? If so, it has nothing whatsoever to do with your issue here… My response was strictly to the original post, I’m not sure what could have given you the impression that it had anything to do with the issue you’re facing here?

If you’re trying to understand where your processing might have gone wrong or could be improved, I’d encourage you to post the exact series of commands that you used to process your data, right from the original DICOM import.

I’d also encourage you to look at your fibre ODFs in mrview’s ODF plot tool, and check that the orientations are as expected – if you’re in any doubt, please post a screenshot of the ODFs for us to have a look at.

Another thing to look at is whether your ROI is in the right place – this can go wrong depending on how it was generated. You can use mrview’s overlay tool to display it on top of the diffusion data (e.g. the FOD image as produced by dwi2fod) to verify that you are genuinely seeding from the place you were expecting.

But otherwise, I’m not sure what the problem is exactly. The results look noisy, but not outrageously so. You might find that using a higher -cutoff value in tckgen than the default will already clean up the results. But otherwise, this just looks like I’d expect probabilistic tracking to look like if seeded from a region like the centrum semiovale – lots of pathways going in lots of different directions in this region, it’s not surprising to find streamlines going all sorts of places. Of course, this all depends on what your seed region was exactly, it would help if you could post a screenshot of that too.