NIMS transition to Flywheel: Part Two

July 17th, 2018
July 17th, 2018

Main point

The Flywheel data management system has been running smoothly for several months at the CNI.  The main purpose of this message is to encourage you to explore Flywheel (https://cni.flywheel.io). A number of groups have already switched from NIMS to take advantage of Flywheel’s features. After Michael completes further testing, which we anticipate to be around September 1, we will stop sending new MRI data to NIMS and instead send data directly to Flywheel (see note). So this is a good time to learn about the new system.

During the Fall we will hold informal sessions at the CNI to explain the system and its features. We will also write more blog posts to explain the system and what motivated us to make the transition.

About Flywheel

Flywheel offers two levels of service, the Center and Lab Editions; the CNI runs the Center Edition. This version does all  the things that NIMS does, including automatically uploading data (e.g., P-files (raw data), DICOM data, and Physio data) and converting data to NIfTI format, which is what most users download.

The Center edition also has features that exceed what NIMS could do. Below is a partial list of Flywheel features that are relevant to CNI users.

  • Session Templates – For each project you can set up rules that automatically check that the expected data were collected, and flag sessions with missing data
  • Notes - Add notes about a session or acquisition (e.g., subject moved; life is good; buy milk)
  • Elastic Search – Find specific types of data, notes, and more
  • Visualization – Flywheel includes viewers for many types of data (NIfTI, DICOM, EEG, OBJ,  CSV, etc.)
  • Collections – Gather data from multiple projects to form a Collection of data
  • Permissions – Adding and removing access to users is simpler, and there are different permission levels available
  • Upload – You can add behavioral data, say from REDCap or or your own notes, to an existing session
  • Gears – Users can run one of a set of Utility Gears (Analysis Gears are available in the Lab Edition)
  • Gear Rules – Users can determine which set of Utility Gears are run on their data. For example, want to use dcm2niix for your DICOM data? Simply setup a Gear Rule to execute dcm2niix for all DICOM data coming in to a given project (ask Michael to show you how, or have a look at the doc).

There are many other features we think CNI users will benefit from. Please explore the interface and browse the documentation available in the UI.

Finally, please reach out to Michael Perry (lmperry@stanford.edu) if you have any questions or experience issues with the platform. In this early phase we expect things to come up and we welcome the opportunity to help navigate through this transition.

Note:  During this testing phase there is a delay before the data appear in Flywheel. Most data are uploaded first to NIMS, where we start most reconstructions and data processing. When testing is completed, in September, Flywheel will handle all reconstructions and data processing while NIMS will switch over to an archival mode.

The CNI Team


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