I am a new user of MRtrix and although I have experience in treating the dMRI signal to find information about the microstructure, it is the first time I am performing tractography.
I’ve started by taking some subjects of the HCP release S1200 and following the suggested pipeline http://mrtrix.readthedocs.io/en/latest/quantitative_structural_connectivity/ismrm_hcp_tutorial.html
Since I don’t have access to a cluster at the moment, the only thing I’ve changed from the pipeline is that I’ve generated 10M streamlines and then I used SIFT command to get 3M streamlines (I thought that this was sufficient to start my analysis).
Since I wanted to investigate some properties in the connection between different areas of the brain I’ve used the given aparc.a2009s+aseg.nii.gz file containing the FreeSurfer parcellation to construct the connectome and here comes my question:
- I’ve notice that some nodes have a lot of connections to themselves (for example in one subject the node 95, i.e. ctx_rh_G_and_S_cingul-Ant, has 15133 streamlines connected itself which is about 0.5% of the total streamlines I’ve created). How should I interpret these connections? Because if I extract them using connectome2tck and I visualise them with mrview I see that they are all kind of “U streamlines” that start and end in the selected ROI without passing through it but passing through different portion of white matter (confirming that the ACT constraint works). Can you help me in the interpretation of those streamlines? Are all of them “anatomically reliable” or should I somehow threshold the results?
Thank you very much in advance.