Image viewer on UKB RAP FSLeyes / ITK-SNAP
For my analyses I would like to be able to open brain MRI scans on the UKB RAP in an image viewer such as FSLeyes or ITK-SNAP. It is important that I can really scroll through MRI scans, inspect the MRI scans visually, and work with the MRI data in the image viewer. Is this possible on the UKB RAP, and how?
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I am curious about this too. For my purpose, I need to be able to outline the different organs in a given image, most likely also through some image viewer. I will keep an eye on this thread and hope for some good inputs :)
Hello Annemieke,
Please see this subsection from the Imaging Data article on the community forum:
"For a more hands-on approach at image analysis, open-source tools such as FSL and FreeSurfer can be downloaded in the UKB RAP. You can find FSL and FreeSurfer pre-downloaded on the IMAGE_PREPROCESSING feature dropdown menu on the JupyterLab app.
There are also multiple visualisation options for both noninteractive and interactive viewing including python packages like pydicom and nibabel (which allow for non-interactive image viewing), and Mango papaya (which allows interactive viewing). Individuals interested in machine learning frameworks may wish to use options like TensorFlow, Pytorch and keras within Jupyterlab. For more information on using JupyterLab in the UKB RAP, please see the UKB-RAP documentation. For more information about image analysis on the UKB-RAP, please refer to this video produced by DNAnexus on image analysis and visualisation methods."
Additionally, you may be interested in seeing our Working with MATLAB on the UKB-RAP article for information on how to use MATLAB on the platform.
We are currently working on ways to improve researcher experience when working with imaging data on the UKB-RAP, and in the near future we will be releasing a community forum article on how to access 3D slicer. Watch this space for further updates!
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