The CLI is a good option for importing large amounts of data. For example, if you have been using XNAT in the past to store data, but now you want all of your imaging data in Flywheel, use the CLI to bulk move the data. Each command for importing is designed for different filetypes. This article explains how to choose the CLI import option based on the data you are importing to Flywheel.
See the CLI getting started guide to learn how to install and log into your Flywheel account through the CLI.
Upload vs import
There are two commands that both get data into Flywheel:
Select an import option to learn more, or continue reading to determine which option is right for your data.
DICOM and PAR/REC files
If you have folders that include DICOM and PAR/REC files, you can use the corresponding import option. The
PAR/REC import options can be used on directories that include other file types. The Flywheel CLI searches for the .dcm or the .par and .rec file extensions and automatically uses the DICOM header information to create or add the files to Acquisitions, Sessions, and Subjects in Flywheel .
See our instructions for how to use these CLI import options:
Directories follow BIDS, Bruker, or Flywheel standard structure
The second type of import options rely on a standard directory structure to import the files in to Flywheel. For example, the
Bruker import use the industry standard directory structure for those data types.
folder import should be used if you are importing data that you previously downloaded from Flywheel, or if you are importing data that was shared from another Flywheel site. The
folder import relies on your folder directory to match the hierarchy within Flywheel. For example:
|Flywheel hierarchy||Example directory for folder import|
To learn more about how to use these import options, see the following articles:
Directories are a mix of file formats
If your directories are a mix of file formats and do not follow a standard structure described above, you can use the
template import to set rules for how to import data. See our directions for how to use the template import.