Coregistration Failure

Dear MRtrix experts,

Hi! I’m a beginner in the field. I am trying to do a tractography on my data, where I ran into several problems. The data was already preprocessed via FSL.

I ran tckgen to do a probabilistic tractography, and got the following:

which clearly has many problems. (I’ve already tried the ‘dwigradcheck’) So we’ve done a quality check, and found a problematic result in the coregistration stage:

The prefrontal cortex is clearly not covered, and the boundary of the grey matter and the white matter doesn’t seem to be expressed correctly.
We are guessing that the coregistering parameters weren’t appropriate for our dataset - do you have any suggestions for changes we might be able to try?
Also we are suspecting that masking or segmentation may have gone wrong too, since the edge of the image is cut off so abruptly.

What may have gone wrong?
Thank you for your help in advance.

Sincerely,
Kelly

Does not look to bad to me. Could it be that you have used a high FA value in the last stage of tbss?

Thanks for the opinion! but unfortunately we didn’t do TBSS on our data…

I have gone through the exact same procedure on a different subject’s data, and found out that the problem wasn’t due to coregistration.

Even for the non-coregistered data (although not shown in the below screenshot), I got an image that has the PFC completely cut off:

so we are suspecting that segmentation, not coregistration, has gone wrong.
If it is so, could you give any advice about what we can fix and try again?

Thank you in advance!

You will have to provide much more detail about your pipeline. What kind of data are you using? What are the exact commands you ran to get to this result?