Streamlines between two ROI

[NeuroSh]

It really depends on precisely what you are trying to achieve.

Particularly, I want to reconstruct streamlines between the dentate nucleus and the thalamus as part of cerebello-thalamo-cortical pathway and dissociate streamlines passing through different thalamic nuclei in the next step. I took the idea of the whole pipeline from palesi, 2015 with minor differences such as creating and defining ROI.

Unfortunately we can’t magically make tractography on clinical data behave identically to tractography on HCP data in all respects

It raised a question for me. If the using methods are not the same for both datasets, is it meaningful to compare them?

@rsmith

1. For streamlines projecting from the dentate nucleus:
2. Select only those streamlines that intersect the thalamus;
3. Those streamlines entering the thalamus should not exit it;
4. The locations of streamlines terminations in the thalamus should be somewhat distributed throughout the volume of the thalamus

Yes, in sum I can say that I aim to reconstruct just a part of superior cerebellar peduncle (SCP). Therefore, It is possible for a tract to go to the cortical regions after passing through the thalamus and not just terminate there, but the path after thalamus is not my interest.

@rsmith

point 2 I would personally use tck2connectome -vector

Frankly, tck2connectome did not work well for my purpose as I wrote in #6. I did not use -vector that time, I’ll try it again. But as you mentioned in #8

@rsmith

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 “ -assignment_all_voxels ”

I interpreted that since in creating a whole brain tractogram, we use gm/wm interface as a seed and dentate nucleus is more a subcortical region located in wm, streamlines starting from dentate nucleus hardly can be reconstructed. As a result, it is necesary to do a targeted tractography in addition to whole brain tractogram. my primary intention was to :

1. Whole brain tractogram with seeding from gm/wm boundary
2. Apply SIFT
3. Targeted tractography with seed and include options.
4. Concatenate pathway of interest with whole brain tractogram
5. Apply SIFT2
6. Select pathways using tckedit
7. Compare both groups

One more question, Can the inability of reconstructing the streamlines with this pipeline be explained by the low b-value?