Is there anyway to check whether the GLM model worked properly or not?
It’s not a matter of whether or not it “worked properly”; that’s the danger with the GLM, it’ll usually do something, but whether or not that something is “proper” is up to the researcher, not the software.
My intuition says:
You’d simply not be exploiting all possible mechanisms for shuffling, and therefore wouldn’t be able to generate as many unique shuffles as you would otherwise, but in most scenarios we don’t process anywhere near the maximum possible number of unique shuffles anyway.
If there were to be any bias in the null distribution arising from the incomplete error modelling, it’s probably smaller in magnitude than the biases that result from using the Shuffle-X method in the presence of nuisance regressors (assuming you have any).
Depends on the extent to which you’re willing to bet the integrity of your research on a stranger from the internet I won’t be offended if you seek clarification from someone with more GLM experience than myself.
I think I managed to merge the updated branch with my local MRtrix3 repository. Thank you for that.
Just beware that the difference between that branch, and what you were using previously, may not be restricted to only the statistical inference commands:
stats_enhancements is based on
dev, which includes myriad changes not yet merged to
Just a small follow-up question, how can I choose to use sign-flipping instead of permutation testing in
fixelcfestats? Is there an option for that? I couldn’t find anything about it in the documentation.
You won’t find it in the online documentation, because that’s generated automatically from the code, and the code used to generate the documentation doesn’t have this capability. If you check the command’s help page by running the command without any arguments, or use the
-help option, that’s the documentation that’s relevant for the particular version of the software you have compiled and are running. Here you’re specifically looking for the