Tractography Error

Dear Mrtrixers,

Hi! I’ve encountered another problem while using our data.
We’ve done a probabilistic tractography and got an incomplete one compared to the tractography that we’ve done in the tutorial.
Here’s a comparison between the two. (left: tutorial tractography, right: our wrong one)

What could have gone wrong!
Please help us with figuring this out.
We appreciate your help so much.
Thanks you so much!

Sujin Park.

Hi Sujin,
This may happen when the x-component of your gradients is inverted (see this thread). Depending on your data, you could use dwigradcheck to try to revert it. This solution worked in my data but I let the rest of the community to check whether this is a correct way to check the x, y and z bvecs:

mkdir dwicheckgrad
mrconvert PA_dwi.nii dwicheckgrad/PA.mif -fslgrad PA_dwi.bvec PA_dwi.bval
mrconvert AP_dwi.nii dwicheckgrad/AP.mif -fslgrad AP_dwi.bvec AP_dwi.bval

cd dwicheckgrad/

mrconvert PA.mif PA.nii.gz -export_grad_fsl PA.bvecs PA.bvals
dwigradcheck PA.nii.gz -fslgrad PA.bvec PA.bval -export_grad_fsl PA2.bvec PA2.bval
mrconvert AP.mif AP.nii.gz -export_grad_fsl AP.bvecs AP.bvals
dwigradcheck AP.nii.gz -fslgrad AP.bvec AP.bval -export_grad_fsl AP2.bvec AP2.bval

mrconvert ../PA_dwi.nii PA2.mif -fslgrad PA2.bvec PA2.bval
mrconvert ../AP_dwi.nii AP2.mif -fslgrad AP2.bvec AP2.bval

Thanks for your reply :slight_smile:
I tried dwigradcheck as u have shown and there was a slight improvement, but guess that wasn’t a cause.
Anyway, I really appreciate ur help. :joy:

Hi Suzan,

It’s often very difficult to diagnose data quality issues if only the end result of a pipeline is shown. Showing some greater detail about the series of steps and the intermediate data may help.

One hypothesis I do have from the image on the right is that you may be using ACT with tissue information having been derived from a very poorly aligned image. This can crop pathways due to that misalignment causing the application of inappropriate tissue priors. I would suggest checking the alignment of multi-modal image information using mrview's Overlay tool, rather than flipping back and forth between images (which can be misleading).


Thanks for your suggestion! I checked the alignment and found out there was a severe problem in the process. The problem was triggered because I used mp2rage image rather than mprage image.

Thank you so much for your help :slight_smile:
I just have to say that your reply has always helped me so much.