Specify the sequence that streamline traverse the include regions



Dear MRtrix’s expert

I’m creating the nigrostriatal pathway using a seed image(SN) and 2 ROIs (GP and Pu), correct pathway start at SN, pass through GP and ends in Putamen, however, it is creating streamlines that pass first through Pu and ends in GP even if I put the inclusion regions in the correct order. Is there any way to specify the sequence that the streamline should traverse?

Thank you very much


Hi, Linlin,

Sorry, I’m not able to answer your questions.

I just curious about how do you extract those ROIs(SN, GP and Pu).
I know FreeSurfer can do subcortical segmentation, however, it is not that precise.

Many Thanks!


Actually, I’m using the probabilistic atlas of the basal ganglia (https://neurovault.org/collections/550/), transform it into native space and using a threshold of 0.1 and 0.2 for SN and GP respectively. The segmentation of Pu is done with FSL.


Wow… 7T structural MRI

Thanks! It looks pretty cool.
Generally, I got the subcortical atlases(MNI-space) , then transform it into native space.

Many Thanks!


Hi LinLin,

There is already an active pull request on GitHub that seeks to provide precisely the functionality that you are looking for. We haven’t yet been able to review the proposed changes or reach a consensus on the desired command-line interface, due to the workload from the 3.0_RC3 update / ISMRM / MRtrix3 workshop, but hopefully we will be able to get this capability into a future release.