DIPY streamline creation with low amplitude FODs


I am trying to create streamlines in DIPY with the following steps:

  • model DWI signal with GQI (creating FODs)
  • plug FODs into DeterministicDirectionGetter
  • plug that dg into LocalTracking

However, when I do this, all streamlines are length 1. If I model the DWI signal with CSD though, I get regular varying length streamlines. Could this be due to the GQI FOD amplitude? This also happened when I modeled the DWI signal with MRtrix’s MSMT-CSD. The FOD’s themselves look good.

I tried running the dg with both from_sh and from_pmf, and set the pmf parameters to min amplitude = 0.0 and min amplitude as a ratio of max amplitude = 0.1. I set max angle to 45. I did everything I could think of to make sure that the streamlines could propagate. The only thing I can think of is normalizing the sh coefficients, but I’m very hesitant to do that as I want to preserve voxel-voxel differences.

Any ideas / help would be greatly appreciated.