With the ISMRM annual meeting coming up in May, I realized that we didn’t have any custom interface for navigating Magnetic Resonance images (~5TB in total) available from Imaging Data Commons - so I (relatively) quickly put one together using Google Cloud Looker Studio.
With this dashboard you can slice-and-dice IDC MR studies by sequence type, manufacturer, field strength, open any of the images that match your selection in the browser, and download any of the corresponding DICOM files - all of which are available without login, direct via S3 API from cloud buckets. Be sure to cite contributors of the data, and follow the license - both of which are also included for the subset you select in the dashboard.
Behind the scenes, this dashboard is powered by BigQuery from a table that contains all of the DICOM metadata for IDC MR studies, searchable via SQL interface. If there are any other MR-specific attributes you would like to see represented in this dashboard, please let me know in the comments!
Very cool! I love that you can even filter by citation so that it’s easy to grab a specific person’s dataset if you’ve read their paper and decided that’s what you want to focus on.
I’m embarrassed to say that this is the first time I actually used idc-index to download some data, but I’m happy to report that installation was quick and painless with no download problems. I do have one question about it though. It mentioned, “Not using s5cmd sync as the destination folder is empty or sync or progress bar is not requested”. Does this mean that if I had some existing data in the folder I ran this from it would check to see if I had already downloaded some of what was in the manifest? Sort of like a “resume” function?
I did notice one minor issue in the dashboard itself. The Size on Disk value summarizing your query appears to always have a “B” (bytes?) at the end rather than indicating MB, GB or TB.
Hope the conference attendees see this and take advantage!
Justin, --use-s5cmd-sync flag is available for some of the download commands (idc download-from-manifest and idc download-from-selection, see Command Line Interface tools - idc-index 0.8.6.dev1+gdeb1239 documentation). I have not added it to idc download. Indeed, with that option it should be possible to resume partial downloads.
I believe that “B” refers to “billions” → “gigabytes”. For that specific widget I set “compact representation” to “auto”, and there is no option to indicate the units, so it is unaware that the original numbers are in bytes. Hope this makes sense!