Hi all
I have noted a few discussions in the forum discussing this or similar issues but I’m still uncertain about how to obtain a fixel mask for a tract of interest that is streamlines/fixels connecting 2 ROIs.
In my case I have 2 ROIs - one subcortical and one cortical and I have tried to seed from one ROI to wholebrain and use tckedit -include for the target ROI to leave streamlines that only connect between the two. But as you note above, there is no clean option to stop the streamlines from leaving that target ROI so you still end up with propagating streamlines.
Here it is suggested to use fixelcfestats -mask option to achieve this but I am not sure how to make such a mask that only contains fixels between the 2 ROIs. I also note the discussion in [How to restrict fixelcfestats to subset of tracts] but here the user already had her defined tract, presumably using a white matter atlas. I am not using a white matter atlas and my ‘tract of interest’ is probably not represented fully by any white matter atlas so I remain unsure how to create a mask of this tract for fixelcfestats.
Would be grateful for your help about how best to generate the fixel mask here?
Thanks a lot
Paul