Self connecting subcortical nodes in connectome analysis

Hi there everyone.

I have found that a few of my subjects have a large discrepancy in the number of tracts which travel between cortical nodes.

I am performing iFOD2 ACT with 10 million streamlines generated which are filtered to 1 million.

After processing the tck2connectome assignment files I found that the discrepancy largely results from tracts with initiate and terminate within the same node. There are so many of these tracts that it drives the number of tracts between other regions down (image 2). These nodes were mostly in sub-cortical areas. This discrepency is present across the Desikan-killianyand and HCPMPP1 parcellation schemes.

Does anyone have any thoughts on why this is occurring?

Many thanks

Hi all, for those that are interested,

I found the problem to be related to the output of 5ttgen freesurfer. As per this discussion 5ttgen fsl vs. 5ttgen freesurfer and this paper (courtesy of Robert Smith and Claude Bajada) 5ttgen hsvs provided a much better result.

It was not without it’s problems. I encountered errors in ~10% of my subjects identical to those experienced here: 5TT hsvs fails in some but not all subjects - #5 by NicDC . The solution at the end of the chain proved very helpful.

Many thanks

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