I built a cohort including T1 structural brain images. However, the actual brain data is in the bulk folder... how can I select all the participants of my cohort in the bulk folder and download the actual data?
As soon as I export the eids for my cohort, I would, for example, start JupyterLab and prepare a script that implements a for loop. It could iterate through all eids (e.g. in file) and for each eid do dx download and unzip operation, as imaging files are typically zipped.
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As soon as I export the eids for my cohort, I would, for example, start JupyterLab and prepare a script that implements a for loop. It could iterate through all eids (e.g. in file) and for each eid do dx download and unzip operation, as imaging files are typically zipped.
As for naming convention of bulk files, I think this will help you a lot: https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/working-with-ukb-data#filename-conventions
An illustrative example of iterating through bulk imaging zip folders is discussed here: https://community.dnanexus.com/s/question/0D5t000004EtXLYCA3/is-there-a-way-to-extract-the-bulk-imaging-data-using- the-spark-jupyter-notebook
It's not 100% ready-to-go for your use case, but with minor tweaks, something similar could work for cohorts with T1 neuroimaging.
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