How to make streamline starting from the GM/WM interface to the pial suface


Hi MRtrix3 experts,

I’m writing to ask about the streamline orientation. I want to track the fiber in cortical gray matter, ideally starting from the gray matter/ white matter interface to the pial surface. Now, I include only the cortex and generate a bunch of fibers. However, I cannot locate starting points and ending points (that saved in .tck file). That is to say, I don’t know if it’s close to the white matter or close to the CSF? Is there any tricks or function that I can use to achieve this?

For example, does the streamline always start from the seeding point? If that’s true, I can seed with GM/WM interface.




Hi Yixin,

The .tck format does not store information regarding the seed point of each streamline; partly because the streamline should ideally not be highly dependent on which particular point along its length happened to be the seed point. However if you are performing unidirectional tracking, then the first vertex of each streamline is always the seed point. If you are doing bidirectional tracking, and absolutely must know the location of each streamline seed, you can use the -output_seeds option.