Fmriprep: starting fmriprep_docker

I am new to Docker and fmriprep. I have read the documentation and am running it on a simple data set. I have encountered some problems with modules not being found. This leads me to think I have done something wrong. I installed fmriprep-docker with pip on my Mac OS 10.12.

$ pip install --user --upgrade fmriprep-docker

The installation worked fine. The run command as stated in the instructions did not work.

$ fmriprep-docker /path/to/data/dir /path/to/output/dir participant

The command wasn’t found. This may make sense sinceI didn’t make any changes to my environment after the pip install. Instead I had to find where pip installed fmriprep. There I found the python file

I then ran the command

/path/to/fmriprep/ /path/to/data/dir /path/to/output/dir participant

and the command ran and started chugging away at my data. I am concerned that the slight difference between fmriprep_docker and is causing my problems that I am experiencing.

Once I know I am correctly running fmriprep_docker I will send additional information about my errors.

Thanks for your help,


Hi @Bob_Kraft,

Thanks for the feedback. I can see two different issues here.

Since you used a user-based installation of fmriprep-docker, FMRIPREP executable files are likely to be somewhere under your home directory, typically under $HOME/.local. You’ll need to add that folder to your $PATH environment variable to use these executable scripts.

Regarding the other errors, it seems you suspect that this is derived from the same issue. Installing without --user should work for you. Anyways, please attach some logs so we make sure this is the case.



Thank you for your quick reply. I will try reinstalling fmriprep-docker and reprocessing my data. Could you please comment on why I need to call and the instructions say to use fmriprep_docker?

If someone knows what they are doing these little differences probably can be ignored. However, for someone like myself who is going through this process for the first time these small subtle differences can really cause confusion.

Thanks again.


By adding --user in your pip install command, you made a custom installation. I am under the impression that no package installed that way will work on your system if you don’t update your $PATH.

With more details on how you defined your environment (anaconda? virtualenvs?..) it would easier to give you clearer pointers.


Also, please add some logs. It is really hard to help this blind…

Thanks again. I didn’t add any logs just because it was a problem with my environment and I didn’t know what logs to add.

As you suggested, I uninstalled fmriprep-docker and then reinstalled it. When I did this I noticed the fmriprep-docker was installed in my /Applications/anaconda3/bin directory. This directory was in my $PATH, which allowed the fmriprep-docker (without .py ) to be run.

Thanks for your patience and clearing up my confusion.


No problem, you are very welcome!