Yes, it looks like you have single-shell data (b = 0 & 1,000 s/mm²), which can’t directly support a 3-tissue decomposition – but your dwi2fod call does request 3 tissue types. This is why the GM segment is coming out all wrong (though I would have expected it to come out closer to straight zeros…).
There are thankfully other options for dealing with single-shell data:
- use the original single-shell CSD method (i.e.
dwif2fod csd). This will only rely on the b=1,000 s/mm² data. - use the new MSMT-CSD solver, but using only one tissue type and one shell (i.e. a 1S1T CSD). This is essentially the same as the regular CSD above, but imposes a stricter constraint on negative values in the FODs produced, at the expense of some loss of angular resolution. This is what is currently recommended in the docs for single-shell data, though I have been planning to update that for a while.
- perform a limited 2-tissue MSMT-CSD decomposition (i.e. 2S2T CSD), using the fact that even a single-shell acquisition actually contains 2 b-values (including b=0), and that’s enough to fit two tissue types – though not the full WM/GM/CSF trio (at least not with that particular command). You’ll find this described at various points on the forum (e.g. here).
- use the SS3T approach noting that this is not part of this project, and not something that we will provide support for).
Hope this helps,
Donald.