I wonder if I made a mistake in the pipeline or if it is normal to have this kind of streamlines …
The latter. This is streamlines tractography we’re talking about
… and I should simply threshold my result to be able to consider self-connections in my connectivity analysis.
Well the connections are there, so the question is whether you should threshold to remove such connections, not consider them; moreover, as mentioned previously, whether retaining or removing them will actually have any effect whatsoever on the analysis.
Is there a chance that these short self connections actually represent somehow the “shorter connection that are entirely within the GM”?
While there’s probably some short connections reconstructed within the WM that are in fact following fibre orientations measured from the GM but spatially extended due to partial voluming, there are likely also short connections within the WM as well; from a naive perspective, whatever is the longest length of individual neurons that are entirely within the GM, I would expect axons of that length and longer to be present within the WM.
I was wondering if we have a mean to detect such structures within GM and I wasn’t able to find any good reference.
There are definitely groups out there trying to do such; but you’d have a hard time having confidence in the reconstruction of such even at the resolution of HCP data. So I’d probably be looking through the ex vivo DW imaging literature.