UKF tractography vs MRtrix CSD in my data

Community SlicerDMRI
1

Hi!
I meet problem when I use UKF tractography in my data. I used the default parameters in Slicer 3D, but the traced out fibres are very discontinuous and even in the wrong direction. For example, the corticospinal tract, pictured below, is broken.

image
image1840×1434 418 KB

I checked my data, it has 3 b-values, 0,1000 and 2000, and each b-value contains 9, 50, 50 directions. A slice of b0 is shown below:
image
image1710×1278 64 KB

I checked different slices in the same direction, and images in different directions of the same slice, and all were fine.
When I use CSD in MRtrix, it works well, like this:
image
image1116×1186 221 KB

So I’m wondering why the UKF method can’t achieve proper tracking on this data?
Looking forward to your reply.
Best regards.

2

Probably something in the gradient directions or measurement frame is incorrect.

3

Thank you. I found that SlicerDMRI can’t handle GE scan headers well?My data has 0,1000,2000 b-values, but I found that using DicomToFSL in DWIConvert, I only get 0 and 2000 b-values.

4

Diffusion scans are notoriously tricky. We suggest dcm2niix since it is actively maintained and DWIConvert is very old at this point.

1 Like
5

Thank you and it works well now.