Tckgen options: seed_image vs seed_dynamic - How does this affect streamlines generated?

Hi all,

I am trying to run tractography to find connections from a specific seed region and targets, and I have been using the MRtrix3 Connectome BIDS app for running my analysis. This involves using the seed_dynamic option to generate tracts throughout the whole brain.

How do I ensure that, using this option, it seeds from all voxels within a specific region and that it effectively captures those streamlines?

How would using the seed_image option, and specifying the mask to be used, change the produced results?

Thanks so much.

Hi Sabir,

With -seed_dynamic, there isn’t really a way to guarantee that it will seed from all voxels within a specified region. However if in the process of trying to reconstruct the whole-brain tractogram, the algorithm observes that there are an inadequate number of streamlines reconstructed within specific voxels, it will place streamline seeds in such a region with greatly increased frequency in an attempt to correct the discrepancy.

If -seed_dynamic fails to generate streamline seeds (that go on to produce acceptable streamlines) within a particular voxel, there’s a good chance that manually placing streamline seeds in such a voxel using some other seeding mechanism will similarly fail to reconstruct acceptable streamlines from such. But as I say, there’s no mathematical guarantee of such.

Certainly if you were to use -seed_image to perform whole-brain tractography, I would expect there to be less seeds placed in such problematic voxels that there would be using -seed_dynamic.


Hi Rob,

Thanks a lot for the explanation, it’s very helpful!