but i get into trouble as follows … The step of statistical analysis of FD does not seem to have been completed (I’ve been waiting more than two days) … Do you have any ideas of what could be wrong?

Throwing an alternative possibility into the mix based on my own experience:

Generally if the system runs out of memory due to the size of the fixel-fixel connectivity matrix, this will occur while the terminal still displays:

```
fixelcfestats: [ xx%] pre-computing fixel-fixel connectivity
```

In your case, this step has completed, and beta coefficient / effect size / standard deviation images appear to have been generated (you should be able to see these in your output directory). Where your program has stalled is in calculation of the *t*-values and CFE enhanced statistics for the default permutation, before generation of the null distribution commences.

In my experience, this normally happens when the design matrix becomes sufficiently ill-conditioned such that the t-values in some fixels become erroneously large (e.g. 10^17), and CFE then effectively stalls as it integrates from 0 to 10^17 in 0.1 increments.

Normally in such a circumstance I would advise calculating the condition number of your design matrix. But if you are genuinely seeing this behaviour in a toy example with 4 subjects and 2 factors only, what’s more likely happening is that somewhere within your template are fixels that contain null values for some / all subjects, in such a way that the GLM code misbehaves and generates enormous / non-finite t-values, subsequently making CFE take forever. What you *can* do is report the output of `mrstats`

on those fixel data files that `fixelcfestats`

has successfully generated.

Rob