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The fw deid Command

To avoid uploading personally identifiable information (PII), use the Flywheel Command-Line Interface to test your de-ID profile on your computer before you upload it.

This article explains how to use the fw deid test command to test your de-ID profile.

Prerequisites

You will need a de-ID profile before continuing. Learn more about creating a de-ID profile.

Instructions

  1. Open a plain text editor such as TextEdit, Notepad, or Sublime.

  2. Copy and paste the following command into the editor:

    fw deid test <SRC> <PROFILE> <PATH> [optional flags]

  3. Replace the placeholders with your information:

    • SRC: The path to the folder to test. This data should be the same or similar to the data you want to upload to Flywheel.
    • PROFILE: The path to file containing the de-ID profile
    • PATH: The path to save test results to on the current machine
    • Optional flags:
      • [--session LABEL]
      • [--subject LABEL]

    Example:

    fw deid test ~/Documents/TestData ~/Documents/deid_profile.yaml ~/Documents/DeIDLogs --subject deidTest

  4. Open the Terminal or Windows Command Prompt

  5. Copy and paste your command into Terminal or Windows Command Prompt and hit enter.

  6. The Flywheel CLI scans your files.

    deidtestexample.png

  7. Once complete, review the log file named deid_log.csv. This gives you a preview of how the DICOM fields would change after de-identification.

    Example:

    deid_logExample.png

  8. Adjust your de-ID profile until the log file shows that your data will be sufficiently de-identified on upload.

Next Steps

Add your de-ID profile to a Flywheel project to automatically de-identify new data or use the CLI to upload data.