If you have existing data from a Bruker Paravision device to import in to Flywheel, use the Flywheel CLI. The Flywheel CLI reads the parameter file to automatically determine subject, session, and acquisition metadata and places the data in to a container in the Flywheel hierarchy.
This article explains how to upload existing Bruker data to Flywheel.
Before you begin
Follow these instructions to download and install the Flywheel CLI. If you cannot download the Flywheel CLI to your computer, you can upload smaller batches of files using your web browser.
Verify that your data is in the Bruker ParaVision format. If your data does not follow the ParaVsion format, see our other options for importing data.
Open Terminal or Windows Command Prompt.
Note the location of the parent folder containing the files you are importing.
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Start with the following command. This command includes all the required flags for importing Bruker data:
fw import bruker <folder containing data> <group_ID> <project_label>
For example
fw import bruker ~/Documents/Study1 Psych "Example Study"Tip
Note: If your project label includes spaces, place quotes around it when entering the command.
Flywheel CLI displays the data it has found and notes where it will import the files. It also notes if the Flywheel CLI will create a new container or use an existing container for the files.
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Add any additional optional flags.
For example:
fw import bruker --audit-log ~/Documents/FWLog ~/Documents/Study1 Psych "Example Study"See our reference guide for more information on the optional flags.
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Review the hierarchy and scan summary as shown above to make sure it matches what you expect.
Note
See below for more information what parameters Flywheel uses to create metadata.
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Enter yes to begin importing. The Flywheel CLI displays its import progress.
Once complete, sign in to Flywheel and view your data,
If you see an issue with the metadata labels, verify that these parameters are correctly configured. This is how Flywheel maps Bruker parameters to Flywheel metadata:
Bruker parameter |
Flywheel metadata |
|---|---|
SUBJECT_id |
Subject label |
SUBJECT_study_name |
Session label |
SUBJECT_abs_date |
Session timestamp |
ACQ_protocol_name |
Acquisition label |
ACQ_abs_time |
Acquisition timestamp |