Then, using tck2connectome and connectome2tck commands, streamlines between thalamus and left dentate nucleus were reconstructed. Now, I think the result seems somehow odd. Based on the literature and biology, I expect more streamlines connecting these two regions.
I tried another way to generate streamlines between dentate nucleus and thalamus, I used LDentate as an additional seed image with inclusion of right thalamus
I think the issue here might relate to the difference in mechanism between how streamlines are assigned to ROIs in
tckedit, and how streamlines are assigned to parcels in
The former relies entirely on testing whether, for any vertex along the length of the streamline, the voxel in which that vertex resides is included in the corresponding mask. As such, a streamline can intersect a ROI at any point along its length to be included.
The latter (by default) deals only with streamlines endpoints, assigning each endpoint individually to the nearest labelled voxel (as long as the distance is less than by default 2mm).
My suspicion is that the dentate nucleus is more-or-less entirely segmented as “white matter” in the 5TT image; as such, streamlines go straight through it, terminate elsewhere, and are consequently not assigned to the parcel corresponding to that structure, because of the mechanism by which that assignment takes place. Therefore for your specific use case the
tckedit approach may be preferable. Though if you feel like going down a rabbit-hole you could try
tck2connectome with “
one more question, in addition to this stage, I want to quantify the results and measure the strength of connectivity between these ROIs
One day I will publish this manuscript, everyone, I promise
I can’t explain the whole thing here, but I would strongly advise carefully reading the SIFT and SIFT2 manuscripts.
In my experience, I found that if you tell
connectome2tck to return streamlines which are connected to nodes 1 and 2, it will return the streamlines that start or finish in node 1 and 2 but do not necessarily connect the node 1 and 2.
Not sure whether or not we disagree on the appropriate usage of the word “connect”
Certainly in the context of the discussion here it’s possible for a streamline to traverse a node without being assigned to it; but rather than considering this as a node that is “connected” to the streamline but to which it is not being assigned, I would instead argue that axons don’t synapse in the white matter, and therefore streamlines shouldn’t “connect” to a node underlying which the voxels are segmented as white matter; rather, there is incongruence in imposed prior expectations between the tissue segmentation and the parcellation data