@opetne thanks for sharing the data. The first dataset
ep2d_diff_mddw_64_p2 seems quite distorted and I didn’t get good results from it.
The second dataset
ep2d_diff_mddw_64_p2_4100_tra looks pretty good. I recognize the major structures anyway (I don’t know anything about canine neuroanatomy!). I followed these steps:
- Diffusion Brain Masking
- Diffusion Tensor Estimation
- Tractography Seeding module (see the “Slicer Neurosurgical Planning Tutorial” linked here).
From your screenshots, I think you did the same except the last step.
The resulting tracts seem ok (again with no specific knowledge). Here is a screenshot:
It was interesting that after each step when I changed the view from trans (red) to sagittal (yellow) for example the blue brain mask was on the new orientation.
I think you may have several datasets open? They have different image sizes, so it could lead to some confusion. Also, you should use the DWI volume
ep2d_diff_mddw_64_p2_4100_tra in Slicer. The other ones with e.g.
_FA in the name are calculated on the scanner, and there seems to be some change in the orientation/origin so the images are not directly comparable.
Your screenshots look good so far, except the mask overlay issue. So, I suggest to work with your dataset
ep2d_diff_mddw_64_p2_4100_tra, and also try some of the example tutorial data from the link above to learn more processing steps. If you have any more questions, please let us know.