Spurious streamlines - difference between tckgen versions

[jdtournier]

To answer your specific follow-on questions:

@Roey_Schurr

I’d be very happy to know if any of you thinks I should be using the default 0.05 for any reason (I should note I’m using SSST CSD, and as far as I can tell, streamlines reach the GM/WM interface.

If you’re using single-shell CSD, then I reckon you could/should increase the cutoff to match what used to be the default. However, I reckon a better option would be to switch to 2-tissue CSD:

• estimate responses for GM, WM, CSF using dwi2response dhollander
• use dwi2fod msmt_csd using the WM & CSF responses only.

This gives you CSF suppression and introduces the hard constraint for the non-negativity, which means your FODs will be a better match to the default cutoff in tckgen

@Roey_Schurr

1. Specifically in the corpus callosum, is it a common behavior for the boundary between CC and the ventricles to be classified as GM, leading to the GM/WM interface image to include these regions?

This will depend entirely on the accuracy of the segmentation, which relies on commands external to MRtrix3. But yes, it’s not uncommon to find voxels containing a mix of CSF & WM (as you’d find lining the ventricles) to be classed as GM…