Cant create a proper FOD?

[jdtournier]

Hi @egemen4552,

Sorry if this comes a bit late – we’ve been busy preparing for and running the MRtrix workshop.

I wonder if your issue is similar to the one discussed in this post:

Mtnormalise nan values as balance factors

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-…

Have a look and see if this is relevant, and let us know if that doesn’t fix the issue.

All the best,
Donald