It is important to remove personal health information (PHI) or de-identify data before importing it to Flywheel. The Flywheel de-identification profile allows you to configure de-identification settings for each DICOM field. Use the profile when you import existing DICOM files via the Flywheel CLI. See our De-identification overview guide for more information on de-identifying data in Flywheel.
This article explains how to use a de-id profile to de-identify data that is uploaded using the Flywheel CLI. This de-identification method is recommended if your dataset has unique de-identification needs. Otherwise, you can add a de-id profile directly to a project, group, or your entire site so all data is de-identified the same.
A de-id profile is a set of instructions for what to do with metadata that may include PHI. De-id profiles can transform or remove standard DICOM tags such as PatientName
, StudyDate
, and PatientAge
, as well as private tags unique to your institution.
We recommend testing the profile on your computer before uploading data. This makes sure Personal health information (PHI) is not uploaded to Flywheel.
The most robust way for implementing your de-id profile is to add it to the CLI config file:
-
Copy and paste the following config template into a plain text editor such as TextEdit, notepad, or Sublime:
##### # Template and Group/Project Settings ##### template: ##### # Optional includes/excludes for directories and files ##### # Patterns of directories to include # include-dirs: # - "*-DCM" # Patterns of filenames to exclude # exclude: # - "*.txt" # - "*.xml" ##### # De-identification Settings ##### deid-profile: custom deid-profiles: - name: custom dicom: #Add de-id profile here.
Under the De-identification Settings section, add the de-id profile you created and tested in steps 1 and 2.
Save the config as a YAML file. For example,
config.yaml
Verify that your config is valid YAML using an online validator tool.
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To use this config file in your command:
$ fw ingest template ~/Documents/DataToImport TemplateExample --config-file ~/Documents/ExampleConfig.yaml
-
You'll see the following output when the Flywheel CLI is using the config file:
$ fw ingest template ~/Documents/DataToImport TemplateExample --config-file ~/Documents/ExampleConfig.yaml $ Reading config options from: Users/AvaFranklin/Documents/ExampleConfig.yaml
Note
CLI arguments override anything set in the config file. For example:
If you add the flag --group Psychology
, but the config file includes the line group: PsychLab
, Flywheel will use Psychology as the group name.