How to run FEAT command using the nipype interfaces package in JupyterLab?

Lidia Fortaner-Uyà

Dear all,

I am trying to run some functional MRI analyses with FEAT command from FSL, using the nipype.interfaces package in JupyterLab.

Specifically, I tried to build the command line following the tutorial provided here. Indeed, trying to run BET following the tutorial step by step, everything ran smoothly. However, trying to run FEAT similarly and waiting for more than an hour, no outputs have been produced. Here below the code I tried to run:

feat_process = fsl.FEAT(
    fsf_file="/opt/notebooks/design.fsf")
feat_process.run()

Is there anyone that has tried to run FEAT with JupyterLab before? Do you have any insigths on why this code isn't running?

Thank you so much in advance to anyone that can help!

Best regards,

Lidia

Comments

3 comments

Date Votes
  • Comment author
    Oliver G The helpers that keep the community running smoothly. UKB Community team Data Analyst
    • Official comment

    Hi Lidia, 

    Thanks for picking up on this. I have just tried and failed to run FEAT myself (I tried without nipype, and with and without parameters, and it no outputs or messages are provided) and I think we have a bug in our implementation on the Research Analysis Platform. 

    I have raised a ticket to the DNAnexus support (Ondrej Klempir) and one of DNAnexus or UKB will post back here when we have further information.

    Many thanks,

    Oliver

  • Comment author
    Lidia Fortaner-Uyà

    Dear Oliver,

    Thank you so much for your contribution! Are there any updates on this issue?

    Looking forward to hear from you, and thanks again for your help and support.

    Best regards,

    Lidia

    0
  • Comment author
    Oliver G The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Lidia,

    Apologies for our delay in getting back to you. 

    DNAnexus have identified that FSL has not been properly configured within the .bashrc profile.

    As a result, on starting the jupyterlab each time, the configuration settings from https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup need to be added to .bashrc. This can be done with the following one line snippet.

    echo -e "FSLDIR=/usr/local/fsl\nPATH=\${FSLDIR}/share/fsl/bin:\${PATH}\nexport FSLDIR PATH\n. \${FSLDIR}/etc/fslconf/fsl.sh\nUSER=root\nexport USER" >>~/.bashrc && source ~/.bashrc 

    DNAnexus have reported the issue to their engineering team, but a permanent resolution may take some time for them to implement.

    I have done some basic testing on this fix using the fsf file linked below, including using nipype, but please report back any further issues you experience with the implementation. https://git.fmrib.ox.ac.uk/falmagro/UK_biobank_pipeline_v_1/-/blob/master/bb_data/template_design.fsf

    Many thanks,

    Oliver

    0

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