Fmriprep: /usr/lib/ants/antsBrainExtraction.sh: line 117: 8754 Killed

[tragus1]

ainCerebellumProbabilityMask.nii.gz
output prefix = highres001_
output image suffix = nii.gz

N4 parameters (pre brain extraction):
  convergence             = [50x50x50x50,0.0000001]
  shrink factor           = 4
  B-spline parameters     = [200]

Atropos parameters (extraction):
   convergence            = [3,0.0]
   likelihood             = Gaussian
   initialization         = kmeans[3]
   mrf                    = [0.1,1x1x1]
   use clock random seed  = 1

/usr/lib/ants/antsBrainExtraction.sh: line 117: 8754 Killed $cmd
Return code: 1

[chrisgorgo]

How much memory is available on the system? Are you running via Docker?

[tragus1]

Hi Chris. 16 GB Ram are available. And I'm running via Docker. Do you have any ideas what's the reason for killing my process?
Thanks!

[effigies]

Can you provide your full fmriprep command and version?

[jdkent]

Bouncing off of @chrisfilo's question, as far as I'm aware, Docker defaults to giving 2GB towards running containers (like fmriprep), so while your system has 16GB, docker may only have access to 2GB. See here for windows and here for mac.

[tragus1]

Thank you problem solved. It was because of the default 2GB RAM Docker gives to containers.