Wrong streamline direction

[Lynn]

Dear Mrtrix Experts,

I used mrtrix to do whole brain tractography and below are some of the results:

1. response function after msmt-csd
   
   
2. fiber orientation direction
   
   
3. streamline using 2nd integration (default tckgen method)
   
   
4. extract corpus callosum using tckedit
   
   
   
   This streamline direction looks wrong but i do not know what the reason could be. Looking forward to hearing from you.

Thanks for your help.
Best,
Lynn

[mia_ming]

Maybe you could list the parameter you use in tckgen which will helps to resolve you problem

[NicDC]

Hello @Lynn,

This is probably due to the diffusion gradient table orientation being wrong - you can run dwigradcheck and correct this in your diffusion data before obtaining the FODs.

You can find example code here.

Cheers,
Nick

[jdtournier]

@Lynn

This streamline direction looks wrong

Actually, I don’t think there’s anything wrong with the directions of the streamlines (i.e. the local tangents). I suspect the issue is more likely to be that the acquisition is not of sufficient quality to resolve the multiple fibre crossings in the centrum semiovale, which the fibres from the corpus callosum would feed into. It’s not unusual to see streamlines heading back down the corticospinal tract like this (I assume this is what you’re concerned about?). This can happen especially when the angular resolution is poor, or the b-value too low, or the overall SNR isn’t high enough, etc.

Can you provide details about your acquisition protocol and the commands you used to process the data?