How to Access and Visualize the Raw Imaging Data on RAP?

Ronghui Yu

Hi, DNAnexus Team! 

Our team would like to use the raw images of Heart MRI from database for model training. We made an attempt in JupyterLab, according to the training videos provided by the Research Analysis Platform(RAP). However, we encountered a coding error that prevented us from accessing and visualizing the raw imaging data. Is there any more detailed methods or specific code to resolve this issue?

Thanks!

Comments

3 comments

Date Votes
  • Comment author
    Melissa L The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Ronghui, 

    You may find the community forum post linked below useful, which contains discussion and links to assist with the visualisation of image files. 

    Is it possible to run the FreeSurfer longitudinal processing pipeline on the RAP for T1 brain images? – UK Biobank

    Thank you for reaching out on the community forum, we hope this is helpful. 

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  • Comment author
    Ronghui Yu

    Hi Melissa, 

    Thank you for your comment, and your suggsetion is very helpful. But we would like to use Matlab for the analysis of the raw imaging data. We also made an attempt in ttyd, but still don't konw how to run Matlab on RAP in detail. 

    The link “A step-by-step tutorial for running Matlab on RAP” posted previously requires a user login to the previous comunity site:

    https://community.dnanexus.com/s/question/0D5t000004AfobvCAB/howto-run-matlab-on-rap

    Would you mind re-posting this tutorial or posting a new one here?

    We are looking forward to receiving your early replay! Thank you!

    0
  • Comment author
    Bernardo de APC Maciel

    Hi!

    I have seen in the webinar it is possible to use Papaya Viewer for interactive visualisation of raw images. Is there any tutorial/code example/best practices recommendations for this? I cannot find any.

    Thanks!

    Best,

    Bernardo

     


     

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