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miykael / fmriflows

fmriflows is a consortium of many (dependent) fMRI analysis pipelines, including anatomical and functional pre-processing, univariate 1st and 2nd-level analysis, as well as multivariate pattern analysis.
BSD 3-Clause "New" or "Revised" License
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Error after pulling #36

Closed limbicode214 closed 2 years ago

limbicode214 commented 2 years ago

Hi there

After pulling the fmriflows docker and the command: docker run -it --rm -p 9999:8888 -v /persistent/home//myHome/example:/data miykael/fmriflows

I get the error message: /neurodocker/startup.sh: line 9: jupyter notebook --port=8888 --no-browser --ip=0.0.0.0 --NotebookApp.token=fmriflows: command not found

thanks for help! mike

PeerHerholz commented 2 years ago

Hi @limbicode214,

thx for bringing this to our attention and sorry for the late reply.

I just checked it on my end and get the same error. @miykael I think the problem is the activation/deactivation of the conda environments. It seems that the container is starting in the default conda environment that doesn't include jupyter and not the neuro one from which the notebooks should be started from.

Cheers, Peer

miykael commented 2 years ago

Hello @limbicode214,

Thank you for pointing to the issue, and thanks @PeerHerholz for reiterating on it. It took me a few days to find the bug, but at the end it was due to some small Dockerfile issue here.

I've updated the code and the docker image, so everything should work again as before. @limbicode214, the command docker run -it --rm -p 9999:8888 -v /persistent/home//myHome/example:/data miykael/fmriflows should now work.

Cheers, Michael