Hello,
I would like to visualize the tracks that have been counted in my connectivity matrix.
I have a set of 100 regions and use the -assignment_reverse parameter.
Is it possible to extract those tracks with tckedit or anything similar with the same criteria that tck2connectome use ?
Thank you,
Céline
I’ve found a way to do this:
tck2connectome with the -out assignments optionconnectome2tck
This way I get the tracks between each pairs of regions as independent tck file and can visualize then in mrview.
Hi Céline,
… and use the -assignment_reverse parameter.
Is there any particular justification for using this over the default? It’s kind of there to demonstrate the fact that there is myriad possibilities for mechanisms to assign streamlines to a parcellation image. If you have big fat parcels that project well into the white matter (e.g. AAL) then it’ll probably do OK, but it’s not something that I’d typically advocate using unless there’s a good a priori reason for doing so.
Cheers
Rob
Hi Rob,
I am working on ferrets and my parcellation is a self-made ribbon between the GM and WM with a random parcellation. What would you rather recommend ?
It depends on the extent to which your streamlines propagate into the GM. If basically all streamlines pass through that GM-WM interface into the GM, then the “reverse search” mechanism may well be the preferable approach. With the default radial search mechanism, if the maximal thickness of the GM were larger than the maximum search distance, then it may be possible for a streamline going all the way through the GM to not be assigned to a node. The counter-example is streamlines that terminate kind of at the GM-WM interface, but don’t quite intersect with the parcellation, in which case with the reverse search that streamline would not be assigned to that nearest node.
This is precisely the kind of non-standard use case I was thinking of when I implemented the multiple different mechanisms for streamline-to-node assignment. 
