The BIDS Curation Gear is provided as part of the gear exchange. Once installed, it can be run against a project from the data or session view by clicking Run Gear, selecting Utility Gear, and selecting BIDS Curation. No additional configuration is necessary, the gear will run against the entire project and will automatically determine whether to run in initial or update mode on a per file basis. Once the gear has run, the BIDS view should be available, and the project and any matched files will have BIDS metadata object in their info. The curation gear can be run as many times as is necessary. After initialization, the only fields that will be changed by the gear are fields with auto_update rules specified, as well as the special properties (valid and error_message)
The gear can be configured with two options, reset and entire_project. The first option will clear the BIDS info object on all assets before curation, thus rematching them to templates. The second configuration option is set true by default, and can be unchecked to only curate a single session instead of the entire project. This is useful if a single session needs to be reset before curating.
We also have a collection of webinars on using BIDS and Flywheel.
- Bids Templating: The BIDS Curation Gear
- Automating BIDS Workflow with Flywheel: BIDS Curated Dataset in Flywheel
Running BIDS Curation on a new session in a previously curated project
The safest way to run curate-bids is be sure to do these two things:
- turn OFF the option called "entire_project", and
- leave OFF the option called "reset" (the default is off).
Here is the procedure:
- Select a session: click on a particular session for a subject, e.g. session “baseline” for subject “B026”.
- With "BIDS View" off, click on the blue "Run Gear" button.
- Click on "Utility Gear".
- Select the "BIDS Curation" gear. The version should be the latest.
- There are no inputs.
- Click on "Configuration" and again, this is the important part,
- Make sure that "entire_project" and "reset" are both un-checked (off)
- Finally, click on the blue "Run Gear" button.
In the worst case, if both are checked (turned on), it will reset all BIDS information for the whole project and re-curate everything. That means that any changes done by hand to the BIDS settings will have to be re-done, including finding the scans set to "ignore". If you don't turn on "reset" but leave "entire_project" on, it may undo certain other changes that you may have done to the BIDS settings. Perhaps you have not changed anything besides the "ignore" setting, and then curating the entire project all at once might be tempting because then you don't have to find each session individually, but the safest way is to make sure that both check boxes are off, just to be sure, and run the gear on each session individually.