Seeding from pre-defined coordinates

Dear MRtrix community,

I will be grateful for your help with the following question. I am interested in seeding streamlines (ideally - using tckgen iFOD2) strictly from pre-defined coordinates which are not tied to the voxel grid (in my specific example - derived from but not representing the coordinates of the vertices of a surface mesh). Is there a way of feeding those data into the algorithm to initiate seeding?

Many thanks,

Hi Dmitri,

If the set of locations from which you wish to seed is reasonably small, what you can do is utilize the -seed_sphere option, but give the sphere(s) a really small radius (e.g. 1e-6mm).

If instead you have a long list of precise locations that you wish to use as seed locations, this has been proposed previously. It’s certainly technically possible, it’s just one of those things that is difficult to give priority to over other things. It wouldn’t be overly difficult for someone reasonably familiar with C++ though, since the code is already quite general so it would only require the addition of one new derived class and one new command-line option.


Cheers Rob, already done using both approaches (combined) :+1: