First time fmriprep user - error in nipype related to FSL debugging

Hi I am new to fmriprep and fmri preprocessing in general. I am running fmriprep through a singularity image. I get this error at multiple steps in the process. Does anyone have some idea of how to debug this?

It seems to me that you are working on a manually prepared environment.

As described in the documentation, you’ll need a fully functional installation of third-party software. However, your installation of FSL seems to be broken.

Fixing your installation of FSL should do, assuming that all the other dependencies are correctly installed.

Alternatively, please consider running containerized versions of fMRIPrep (

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hi! i am running it through a singularity image actually and ran it with the singularity run command. This makes me think though. I didn’t use --clean-env because I wanted it to see my $FS_LICENSE environment variable. But, I do have a version of FSL installed on the HPC… maybe it is getting confused about which one to use?

That is certainly the case.

Although some HCPs do not honor this magic, you can introduce environment variables in the container by exporting them with the prefix SINGULARITYENV_. You can use this trick in combination with --cleanenv.

On your case, make sure you include the following in your submission script:


For further tips and tricks: