Neurodebian docker usage

What happened

Hi guys,

I find that i have some difficulty understanding the usage of neurodebian docker containers. I searched for documentation but did not find much. Maybe if you could point me to some documentaion that would already help.

The docker page states: “NeuroDebian images only add NeuroDebian repository and repository’s GPG key.”

Right, very well. But: after pulling the docker image, there is no software installed as expected. However, one cannot apt-get any of the usually packages either. manually adding the repo from nerodebian page does not change anything either.

Maybe i fundamentally misunderstand the concept. could someone clarify?

Command used (and if a helper script was used, a link to the helper script or the command generated):

docker pull neurodebian

docker run --rm -it neurodebian

apt-get install fsl
  Reading package lists... Done
  Building dependency tree... Done
  Reading state information... Done
  Package fsl is not available, but is referred to by another package.
  This may mean that the package is missing, has been obsoleted, or
  is only available from another source



Environment (Docker, Singularity / Apptainer, custom installation):

well docker
on macOS and ubuntu 18.04 and 22.04

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Relevant log outputs (up to 20 lines):


Screenshots / relevant information:

Hi @thoern, I can’t comment on general neurodebian topics, but I would strongly recommend against installing FSL via neurodebian, as their version is woefully out-dated. Instead I would suggest using our installer script, as described at

Dear Paul,

Thank you, your point is well taken. However, i used fsl just as an example here. The behavior described is a consistent problem for all neurodebian packages i tested, e.g., afni, python-nipype, …