One thing to note is that my dataset is all pathological brains (stroke), which I did not explicitly mask out in any steps. The DTI data has 2 unique bvals (b = 0 and b =1000), and I did multi-shell multi tissue CSD, only using the white matter and CSF response functions.
I’m wondering why my tract segmentations seem so far off? I attached the tract segmentations I got for the corpus callosum (entire thing), as well as the left corticospinal tract - they don’t look accurate to me.
This is my first time working with fixel based analyses, so I really appreciate any help! Thanks so much.
I don’t have an answer to your main query, but I am working with a dataset with similar bvals and I noted that doing a single shell multi tissue CSD pipeline provided much better outputs.
Single shell data worked fine with the multishell pipeline in my own little experience. Regarding the strokes, if no lesions are in the FOD template, I’m not sure it would affect TractSeg’s anatomy-based segmentation substantially either, though I could be wrong.
What I would suggest is rather looking at your TractSeg pipeline and at the 3D tracks it generated. Did you obtain the masks from the latter? Are these fixel masks loaded as overlay in mrview? Plotting tracks or the masks as fixels instead of overlay images could make more sense as you visually get the directions in mrview.
I simply meant in terms of FOD. SS3T version is only slightly different from MSMT approach (but you can see more green - csf areas)–> MSMT approach with CSF tissue ditched is very sparse and possibly leads to reduced number of fiber tracks at streamline step. I did a comparison of SS3T vs MSMT (without CSF) vs MSMT (with CSF).
