Fixelcfestats killed

Dear MRtrix Users,

The final step of Fixel-based was killed. My voxel size is 1.15 and I have 678338 fixels. The error is as follows:
[ 16%] pre-computing fixel-fixel connectivity… Killed

I have a 64g ram. Does anyone have any solution for this?


There’s a little bit in the documentation here and here about this. Your voxel size is a little smaller than the current recommendation, and the fixel count is correspondingly larger, the latter of which strongly influences the memory requirements. The tracking parameters used for tractography on the group average template can also influence the total amount of fixel-fixel connectivity and hence the amount of memory required.

There’s a large impending update to MRtrix3 statistical inference code here. One small but highly consequential piece of these changes is a substantial decrease in the amount of RAM required by fixelcfestats. You could try that, though I don’t know if the savings would be enough to successfully execute with your current data. Also note that the RAM reduction is not the only change in that code; there are a lot of other changes to the GLM and surrounding code, which you would need to read and be aware of if you were to utilise the results from such.


Hi there,

I am also having a similar issue, but I am unsure why the process is being killed during the permutation process when I run fixelcfestats. I am following the fibre-density and cross section manual. Here is the feedback error (which I get for running all three of the fibre density metrics), below:

fixelcfestats: [  3%] Running permutations...e[0Ke[?7hfixelcfestats template/fd_smooth/ files_fd.txt stats_matrices/design_matrix.txt stats_matrices/contrast_matrix.txt template/matrix/ stats_fd/: Killed
fixelcfestats: Number of fixels in template: 794289

Here is a little bit of information about my data and computer:

  • My number of fixels is at 794289 (checked via mrinfo -size directions.mif on the fixel mask)
  • I upsampled the dwi data to 1.25 voxels
  • I have 96 GB RAM on my virtual machine

In a previous analysis, I was able to run fixelcfestats when I had around ~800,000 fixels. I have since then added in more data (N + 57), but I believe that this would not affect this process or the memory so much. I also manually edited the template mask, as it was not including some brain regions on the white matter fod template. I then checked that the template mask, the sifted whole-brain tractogram (2 million tracks), and the fixel mask was sensible and not including any non-brain regions. I am a bit stumped, and so any advice on why this is occurring would be appreciated – thanks!

Ahh wait, I think I found the problem - I am not supposed to add regions to the group template brain mask, as suggested in the manual. So, I think I need to go back and edit the individual brain masks, and then re-run the analysis.