Spurious streamlines - difference between tckgen versions


#1

Dear all,

I’ve encountered a problem with the output tckgen, somewhat related to the one reported here:

I ran tckgen with ACT using a command like that:

tckgen -algorithm iFOD2 -act 5ttf.mif -seed_gmwmi 5ttf_gmWm.mif -backtrack -crop_at_gmwmi -select 500000 csd.mif tck500000.tck’

In the result, I noticed some spurious streamlines going in the anterior-posterior direction within the splenium of the corpus callosum (and other regions), as well as possibly spurious streamline within the cingulum bundle, going in the medial-lateral direction and in the ventral-dorsal:

I am using an up to date version of MRtrix. When typing “tckgen --help” the version I get is:
MRtrix 3.0_RC3-51-g52a2540d tckgen Jun 14 2018

Importantly, most of these spurious streamlines are absent when using a different machine with the following version:
MRtrix 3.0_RC2-90-g21f3d913-dirty tckgen May 22 2018

as can be seen here:

Is this behavior the result of a recent update to tckgen? Should I downgrade to an older version, or perhaps this is the side effect of a second, wanted behavior?

Any help would be greatly appreciated.
Many thanks!

Roey


#2

Hi everyone,

Indeed, this seems to be the result of lowering the default FOD -cutoff threshold used by tckgen, from 0.1 to 0.05. See also a discussion about changing this default parameter here. When changing the cutoff from 0.05 to 0.1, the results look at before (no anterior-posterioe streamlines within the corpus callosum).

  1. I’d be very happy to know if any of you thinks I should be using the default 0.05 for any reason (I should note I’m using SSST CSD, and as far as I can tell, streamlines reach the GM/WM interface.

  2. Specifically in the corpus callosum, is it a common behavior for the boundary between CC and the ventricles to be classified as GM, leading to the GM/WM interface image to include these regions?

Many thanks,
Enjoy ISMRM and OHBM,
Roey