3D Slicer on UKB-RAP: Outdated

Bethan Data Analyst

Hello! This community forum thread is now outdated. 

Previously, the article ‘3D Slicer on UKB-RAP’ guided researchers on how to access 3D Slicer through the UK Biobank Research Analysis Platform. Since then, the platform has been further developed and now allows researchers to access 3D Slicer directly within UKB‑RAP. Instructions for the updated workflow can be found here:

Viewing images on UKB-RAP with 3D Slicer

If you have any additional knowledge, questions, or difficulties related to this new process, please create a new forum post. 

Thanks for using the community!

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3 comments

Date Votes
  • Comment author
    Bethan Data Analyst
    • Edited
    • Official comment

    If you are experiencing issues, please refer to the troubleshooting steps below.

    1. Trouble Starting a Cloud Workstation

    • Ensure you have the latest version of the DNAnexus (dx) toolkit installed.

    2. Trouble Connecting via SSH to Your Cloud Workstation

    • If your VPN is active, try launching and connecting to your job with the VPN turned off.
    • Avoid connecting to your job too early. Confirm your job has fully launched via the Monitor tab in your UKB-RAP project, prior to entering your dx ssh command.

    • Reconfigure your SSH keys and verify that all required files are present. You can do this by running:

      dx ssh_config

    • Try to initiate your SSH connections in a new terminal window.
    • Attempt to switch between networks (e.g. home vs. university/office) to rule out firewall issues. Contact your IT department in the event of a firewall issue at your institution.
    • If you have access to another UKB-RAP project with dispensed data, try launching a job there to check if the issue is project-specific.

    3. Trouble Clicking 'Next Sample' in MONAILabel

    • Ensure your selected directory contains only NIfTI format images.
    • Confirm that you are using NIfTI images, not DICOM images.
  • Comment author
    Astrid Filt

    Hi Bethan

    When starting an instance of the cloud workstation, I cannot see any ec2 address after the step:

    >>> dx describe job-<Insert Job ID here>

    It says that I should make note of the ec2 address labelled as ‘host’. 

    However, there is nothing labelled ‘host’ in the list of metadata. I have inserted a screenshot of my options below. Can you help me as to what I'm doing wrong, or perhaps what I'm looking for?

     

    Thank you in advance :) 

     

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  • Comment author
    Bethan Data Analyst

    Hi Astrid Filt , thanks so much for your question! You're off to a great start. Finding the ec2  address can cause a little bit of confusion, since it can take a bit of time for ‘host’ to appear when running dx describe . This is because your job needs to be in state ‘running’ for the host ec2 address to appear. I would recommend running the dx describe command about 5-10 minutes after starting your instance. You should then be able to find it underneath ‘allowSSH’ and above ‘sshPort’-- I will attach a screenshot for example!

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