How to Access/Download Bulk Data from RAP
Hello everyone,
I’m a beginner in MRI research and I’m currently working on a project where I need to access/download bulk data from the Research Analysis Platform (RAP). Specifically, I’m interested in field 25752, the rfMRI partial correlation matrix, dimension 25. This isn't raw imaging data but a text file containing matrix data.
Could anyone provide detailed guidance on how to access or download this particular data through RAP? Any specific paths or code snippets that could be used to retrieve this data would be greatly appreciated.
Thanks in advance!
Comments
2 comments
Hi Jian,
Thanks for your post.
We recently announced changes to how UK Biobank data is accessed and as part of these changes we now require researchers to complete mandatory training courses.
You can find a copy of this announcement and the related FAQs here:
https://community.ukbiobank.ac.uk/hc/en-gb/community/posts/19996604847133-Changing-the-way-UK-Biobank-data-is-made-available-to-researchers-around-the-world
https://community.ukbiobank.ac.uk/hc/en-gb/categories/19950747200413-UK-Biobank-Research-Analysis-Platform-UKB-RAP
For help using the UKB-RAP, please see this guide created by DNAnexus:
https://www.dnanexus.com/partnerships/ukb-rap-user-help-center
One way to work with the matrices is to open a JupyterLab instance from the Tools tab, copy the matrix files from your main project storage (in folder Bulk/rfMRI) into the instance storage, and then use a python notebook. There is an example Notebook called “A109-Find Imaging Bulk Files” that might be useful, see https://github.com/UK-Biobank/UKB-RAP-Notebooks-Access/blob/main/JupyterNotebook_Python/A109_Find-imaging-bulk-files.ipynb .
For more detail on the UKB_RAP in general, see the documentation at https://dnanexus.gitbook.io/uk-biobank-rap .
For more on using JupyterLab instances, see https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/using-jupyterlab-on-the-research-analysis-platform .
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