Hi MRTrix forum, I have a rather baffling issue at the moment.

We recently converted our FBA pipeline from `v3.0_rc3`

to `v3.0.2`

to take advantage of the improved GLM capabilities in `fixelcfestats`

. (While we were at it, we also added some other niceties like bash parallelization.) Rerunning from the raw data, we get essentially equivalent results at each stage, accounting for a couple of non-deterministic steps in the process, however, when it’s time to actually run `fixelcfestats`

, things fall apart.

Specifically, the `uncorrected_pvalue.mif`

and `fwe_1mpvalue.mif`

files come back with nothing but zeros:

```
$ mrstats fwe_1mpvalue.mif
volume mean median std min max count
[ 0 ] 0 0 0 0 0 164577
```

The `tvalue.mif`

and `Zstat.mif`

values also come back as all zeros. After re-checking each step of the process, sometimes redoing steps by hand to ensure that there wasn’t simply a flaw in the script, I found a couple of odd things that I hope will help diagnose the problem:

- For some reason, after the
`dwinormalise`

step,`fa_template.mif`

and`fa_template_wm_mask.mif`

have different numbers of voxels:

```
$ mrstats fa_template.mif
volume mean median std min max count
[ 0 ] 0.0381717 0 0.104609 -0.0280504 0.908895 782582
$ mrstats fa_template_wm_mask.mif
volume mean median std min max count
[ 0 ] 0.0196256 0 0.13871 0 1 973370
```

This did not happen with the old pipeline:

```
$ mrstats fa_template_old.mif
volume mean median std min max count
[ 0 ] 0.0325751 0 0.0978714 -0.00965092 0.923676 980796
$ mrstats fa_template_wm_mask_old.mif
volume mean median std min max count
[ 0 ] 0.0209177 0 0.143109 0 1 980796
```

Despite this, the `fa_template`

and `wm_mask`

do seem to overlay correctly in `mrview`

, so this could simply be a quirk of a change from `v3.0_rc3`

to `v3.0.2`

. The newer pipeline did give me marginally more brainstem, but that seems deeply unlikely to be causing this kind of problem.

- The
`null_contributions.mif`

files come back with a single voxel (or fixel, I guess) of 5000 (i.e., the default number of permutations.)

```
$ mrstats null_contributions.mif
volume mean median std min max count
[ 0 ] 0.0303809 0 12.325 0 5000 164577
$ mrstats null_contributions.mif -ignorezero
volume mean median std min max count
[ 0 ] 5000 5000 N/A 5000 5000 1
```

Again, this did not happen in the old pipeline:

```
$ mrstats null_contributions_old.mif
volume mean median std min max count
[ 0 ] 0.0307365 0 0.212712 0 21 162673
$ mrstats null_contributions_old.mif -ignorezero
volume mean median std min max count
[ 0 ] 1.16144 1 0.629731 1 21 4305
```

This seems potentally more indicative of…something, but I am unable to understand what. Does anyone here have any advice or insights? I feel like there’s something obvious I’m missing but after spending several days trying to track down the problem myself, I’m stumped.

**Edit**: Another thing that occurred to me is that the stats seem to run much faster on the new pipeline than the old. Would that correspond to whatever process is giving me all zeros on everything? It seems reasonable.