Fmriprep installation issues: nibabel


I’m trying to install fmriprep but I keep getting this error:

Cannot uninstall ‘nibabel’. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

What can I do?

Thanks for your help!


Could you provide the full console log with the command you are using to install FMRIPREP?

$ pip install fmriprep

Thanks. We do not recommend this approach to installing fmriprep. Instead please consider running fmriprep via Docker or Singularity.

Hi Chris,

Thanks for your response. Does fmriprep allow us to customize the nipype workflows? For example, if I want to add/edit certain arguments?

Yes of course - it’s an open source project licensed under BSD. Code is available at You are free to modify it as you see fit, but I encourage you to send us a Pull Request on GitHub if you add a new feature or fix a bug so other users could benefit from your work.

Thanks for your help, Chris!

If you installed nibabel with one of the various conda flavors, you should conda remove nibabel before installing fmriprep.

Otherwise, manually remove the package first pip uninstall nibabel to then install fmriprep.

It seems that your environment is a bit old as distutils is being deprecated. You will likely get more similar messages referring to other packages. The solution would be exactly the same.

That said, I would highly recommend using containers for fmriprep.

Thanks for the response! I was able to manually remove nibabel.
I will look into containers for fmriprep. What I can’t wrap my head around is how I can run my customized scripts on docker/singularity. This is my first time using containers and fmriprep so please forgive my silly questions!

If you’re specifically trying to run a modified version of fmriprep in docker or singularity, I’d look at the documentation for developing with fmriprep.

More generally, @ChrisGorgolewski has developed some really great resources for getting started with containers !

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Thanks for the links, very helpful! :slight_smile: