Even though I left the implementation there, as I described in another thread, I don’t think I’d actually advise using -assignment_forward_search; it’s there for conceptual demonstration more than anything else.
The gap shown in the pictures may also be due to the decimated .tck file used for visualization purposes, it may be the whole track vol would fill the gap better.
This depends on what you mean by “decimated”. If you’re just reduced streamline count, then that’s unlikely to “close the gaps”, given that you are showing enough streamlines such that gaps do not appear between them elsewhere in the image. If in reference to vertex downsampling, whether explicit via tckresample or implicitly within mrview (which happens seamlessly), the endpoint vertices are always preserved.
One option, for the future, would be to make
labelsgmfixdependent on5ttgenoutput
There isn’t enough information in the 5ttgen output for labelsgmfix to do its job. What’s needed (and would be more faithful to the software tools being utilised) would be for FSL’s run_first_all to be executed first, and then its output utilised by both 5ttgen and labelsgmfix.