The tractography trajectories from mouse dMRI do not match the projection pathways visualized by high-titer viral tracing

1

"The dMRI tractography trajectories in mice do not align with the projective pathways visualized by high-titer viral tracing. I have attempted various parameter combinations, but the discrepancies remain significant. The current dMRI data for the mouse has an isotropic voxel resolution of 200 μm.For dMRI tractography, the seed region was defined by dilating the viral injection mask in the mouse primary motor cortex until it reached the adjacent white matter. Now, I have two questions:

① How should the dMRI tractography parameters be adjusted appropriately? What specific suggestions do you have?

② Is it necessary to incorporate 5TT (five-tissue type) constraints for tracking?"

The script is as follows:

tckgen msmt.nii.gz 1.tck
-algorithm iFOD2
-cutoff 0.1
-minlength 3
-maxlength 20
-angle 30
-step 0.05
-select 50k
-seed_image “$injection_mask”
-mask “$brain_mask”
-force

I look forward to your reply.

2

I guess the first question is if other tracts have the expected shape. If the corpus callosum or the anterior commissure do not look the way you expect, then there is probably something wrong with your data..Frequently, vector orientations are incorrect due to conversion issues. Check your V1 maps using the fixel viewer, or load the diffusion tensors in the ODF tool. If these two tracts look normal, then please provide a snapshot of the resulting tract.

Also, singe your seed_image appears to be an injection mask, I am assuming that you are seeding the gray matter. Try reversing your approach, seeding in the white matter and using your injection mask as an endpoint (`-include` ROI). Alternatively, reduce your `-seed_cutoff` value.

I do not think 5TT would be of much help.

Good luck.

Luis