Streamlines between two ROI


Dear MRtrix experts,
I created a whole-brain tractograms using pipeline described in BATMAN tutorial. Now, I want to obtain streamlines between the cerebellum and thalamic nuclei. I got masks of cerebellum and thalamus from atlases and transformed them to individual space. I used tckedit

with -include option, but the result is not the one that I aim for. Also, I tried -mask option but it does not show me the connections between two regions.
Here is the result for -include option:

Could you guide me on how can I remove unwanted streamlines that go from thalamus to frontal region?


I did a almost same thing of making a few ROI connectivity.
The extraction of specific bundles is done by tck2connectome and connectome2tck command as know as I know.


Thank you for your reply.
I think tck2connectome needs a parcellation image, as I reed in Tutorial. I do not know any atlas that has thalamic nuclei and cerebellum together. I got cerebellum atlas from SUIT package and thalamic nuclei from Morel atlas. Is there any way to combine them?


It’s certainly possible to combine parcellations from different sources (as long as they don’t overlap). But it’s not something for which a push-button command solution is provided: you need to figure out exactly how the images you have need to be combined together in order to produce an image where each parcel contains an integer index label, and the indices of the different parcels increment from 1. So for instance, if you had one image with parcels labelled 1-10, and another with parcels labelled 1-20, you could use mrcalc to add 20 to the values in the first image, then use mrcalc or mrmath to compute the sum across the two images; you would then have a single image with parcels uniquely valued from 1-30.