Tckgen - termination mask



Dear experts,

with tckgen, I would need to terminate my streamlines once they are leaving the specified region. In probtrackx this feature is called “termination mask”.

I could overcome that by creating whole whiter matter mask and supply it as -mask option, but that is cumbersome, since I do not want to constrain how my streamlines can enter my termination mask.

Do you have any clues how to do it with my current tckgen version (3.0_RC2-82-gbb77205e)?

Antonin Skoch


Eeek… that’s an awkward one. Let’s see if my interpretation here is correct:

  • Streamlines can propagate and terminate entirely outside the termination mask.

  • Streamlines can propagate and terminate entirely within the termination mask.

  • Streamlines can propagate from outside the termination mask into the termination mask.

  • Upon entering the termination mask, streamlines are still free to terminate at any point within that mask due to other streamlines tractography criteria.

  • If a streamline attempts to propagate from inside the termination mask to outside the termination mask, it is terminated due to the constraint imposed by having provided that termination mask.

If that’s the case, the closest thing I can suggest would be to define a 5TT image where what you define as a “termination mask” is labelled as sub-cortical grey matter. Streamlines will be forbidden from entering and then exiting that region by ACT prior #6. (They will however be truncated and so the termination may no longer be exactly at the point where the streamline attempted to exit the mask, but this is something that could be temporarily disabled short-term / controlled by a command-line option flag long-term.

Otherwise, it’s a slightly clumsy functionality to even define appropriately; so I’d be curious to know whether this is simply a feature that can be used to serve your purpose that you’re looking to duplicate in MRtrix3, as opposed to having a purpose that needs serving but could be achieved in some other manner using either existing or more appropriate methods.



Dear @rsmith,

my goal is following: I want to do FBA but I want to restrict my FBA to fixels located in the region of a specific pathway (for example acoustic pathway between Inferior colliculus and Heschl gyrus). So I need to provide streamlines connecting these two structures, but I want to restrict streamlines propagating outside the connection of these two structures (i.e. in case of acoustic pathway I do not want streamlines to continue to propagate from inferior colliculus more inferiorly to the brainstem and in cortex I do not want them to propagate outside from the heschl gyrus mask more distant to the periphery of the temporal lobe). Ideal is to crop the streamline once it enters the ROI on both sides.
As you are suggesting ACT, I am wondering, is ACT compatible with other features, such as -include, -exclude and -seed_image?
Or maybe the -stop parameter is what I am looking for. Do you think that the following could achieve my goal?

tckgen wm_fod.mif -seed_image inferior_colliculus.mif -include heschl_gyrus.mif -exclude excludion_region.mif -seed_unidirectional -stop