The target is to get the voxel to voxel connectivity matrix between left thalamus area and left M1 area.
Can I infer from this that you want, for every voxel in the left thalamus, a vector of connectivity values, one value per voxel in M1?
If that’s the case, what I would suggest is trying this script. Provide a thalamus mask as the region of interest from which streamlines will be seeded. For the parcellation image, what you would need to do is produce an image where every voxel in M1 contains a unique integer value. I don’t know of an existing command to do this, but it would probably not be very difficult for anyone with a little bit of coding ability to produce.
tckgen -algorithm iFOD2 -seed_random_per_voxel L_tha.mif 50 -act 5tt_coreg.mif -backtrack -seed_undirectional wmfod_norm.mif ltha_all.tck
If you want to characterise the connectivity to every voxel in M1 independently from every thalamic voxel, you are going to need a lot more than 50 streamlines per voxel. The numbers need to be large enough to counteract the stochastic nature of the tractography algorithm; and when quantifying voxel-to-voxel connectivity, this number will be huge.
- Is the coordinate of streamline txt file described in the image coordinate for all the voxels that are included in the individual streamline?
In MRtrix3 streamline vertex locations are defined in real / scanner space. This is independent of any particular image voxel grid.
I’m looking for the streamline to contribute node-to-node connectivity for all voxels from seed region to target region traversed by that streamline.
This actually sounds like the converse of what you described in the first post. Whether or not a streamline contributes to the connection strength only between the two voxels in which the two streamline endpoints reside, or whether the long list of voxels intersected by each streamline is constructed and then the voxel-voxel connectivity is incremented for every possible pair in that list, is a crucial detail that influences how such calculations can / should be performed.