Do you spend a lot of time preparing your data for use? Flywheel Gears reduce data-management overhead by automating many routine, time-consuming tasks.
Gears are applications that run in Flywheel. They come in two flavors depending on their functionality: Utility or Analysis. For example, to convert all files from DICOM to NIfTI format or produce a report on QA metrics like displacement and signal spikes, you can use a Utility Gear. Or use an Analysis Gear to run popular tools such as Freesurfer.
Learn more about how Gears can reduce your data-management overhead and allow you to focus on the research.
To view the available Gears in your environment, click Installed Gears in the left navigation menu.
Site Admins can add more gears in two ways:
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The Gear Exchange: The Gear Exchange is a curated collection of Gears maintained by Flywheel. These Gears are made available through the contributions of Flywheel employees, customers, and members of the broader research community. Browse the the Gear Exchange for more information, and contact Flywheel Support to add these Gears to your site (only Site Admins can install Gear Exchange gears.)
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Develop your own Gear: You can also create your own custom gear to upload to your site. See our Gear Developer tutorial for more information on how to build your first gear.
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Navigate to a session, and click the checkbox.
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Select an acquisition.
Tip
Batch run GearsTo run a Gear against multiple sessions or acquisitions at the same time, use batch processing
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Click Run Gear.
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Select Utility or Analysis.
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Choose a gear from the list.
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Select any inputs.
Tip
You can also add a tag to the Gear job. Tagging Gear jobs is helpful for tracking.
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Select the Configuration tab to edit any additional settings.
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Click Run Gear.
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View the Gear's progress by clicking the Provenance tab. If you do not see the gear, click Refresh.
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Once the job is complete you can view detailed logs, including the input and output files for the Gear.
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If you ran an Analysis Gear, you can view the output in the Analyses tab.
However, manually running a gear each time you have new data can be time consuming. To simplify running Gears, create Gear rules to automate jobs.
Gear Rules allow you to automate a project's data processing. Whenever the conditions of the gear rule are met, the rule triggers a specific gear to run.
Create a simple project gear rule to automatically classify DICOM files:
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Click Projects in the left navigation menu.
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Select the options menu
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Click Add New Rule.
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Enter a name for the rule
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Under If the data matches ALL of the following criteria, Select file type from the list.
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Enter dicom for the file type.
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Click Select Gear.
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Choose SciTran: MR Classifier.
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Select a version of the Gear to run. In most cases you should use the latest version.
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Disable Always use the latest gear version.
When this is enabled, Flywheel automatically updates the gear when a newer version is published. However, updating the gear version may have unintended consequences for provenance and may change how the gear works.
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Modify the Gear configuration if necessary.
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Click Save Changes.
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Click Save on the Gear rule.
Now, each time a DICOM file is added to the project, Flywheel will automatically run the DICOM MR Classifier. Correctly classifying data and extracting metadata greatly increases the value of raw data and allows you to do more with it inside Flywheel. For example, now that your data is properly classified, you can create more gears rules to automate converting DICOM files to NIfTI using the
dcm2niix: DICOM to NIfTI conversionGear.