Bidirectional fibers



After seeding a several number of fibers from a given ROI, I realized that the voxels closer to the ROI are saved not only in the first raws of the but also in the last raws for certain fibers. I thought that the first voxel has to be inside the ROI mask or at least in the vicinity of it, but it doesn’t seem to be the case… Could you explain what it is due to ?

Fiber 1:

Fiber 2:

Thank you in advance


Assuming you’re not using either the -seed_unidirectional or -seed_direction options in tckgen, then streamlines will be bidirectional, and start in random directions. This means that the algorithm will first start from the seed region along some random direction, track as long as it can, then flip the streamline back to front and start tracking along the opposite direction from the seed point. So half the time, it will start in a ‘forward’ direction, half the time in the opposite direction, which would explain what you see.

If you specify -seed_direction, then you can guarantee that the streamlines always start in what you consider the ‘forward’ direction, which should mean that they all behave as you expect. If you use the -seed_unidirectional option, then the half of the tracks that start in the ‘wrong’ direction will be discarded, so those left will again behave as expected.

I hope this at least explains what’s likely going on…?


You’re right, I’m not using these two options. Thank you for the tips !

I have however another question. Are the “wrong fibers” wrong in biological terms or not? I mean, if I just flip the column up to down in order to keep all the fibers, as though they all started from the ROI, would it be correct regarding the brain anatomy and connections in the white matter? Or should I however eliminate them?

Thank you


Yes, absolutely nothing wrong with them. If you think about it, these streamlines were reversed internally within tckgen anyway, so there’s no reason you can’t ‘un-invert’ them manually if you want to. They’re strictly equivalent to having started with the opposite seed direction.