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Image De-identification ETL 📸

The Image De-identification ETL is a WIP tool to assist with reading DICOM images from Orthanc, conversion to anonymized NIfTI images, and uploading to Flywheel.

Getting Started

Dependencies

Instructions

First, copy the following file, renaming it to .env in the process:

$ cp .env.sample .env

Then, customize its contents with a text editor:

  • For AWS_PROFILE, follow these instructions to configure a named profile for yourself. Use https://d-906762f877.awsapps.com/start as the SSO start URL and us-east-1 as the SSO region. Assign the name of the profile you create to the value for AWS_PROFILE.
  • For FLYWHEEL_API_KEY, generate an API key from your Flywheel user profile.
  • For FLYWHEEL_GROUP, specify either d3b or an alternative group created for testing (e.g., your name).
  • For ORTHANC_CREDENTIALS, use your Orthanc username and password specified like username:password.
  • For ORTHANC_HOST, specify the hostname (minus http(s)://) that you use to access Orthanc.
  • For PHI_DATA_BUCKET_NAME, specify the bucket name where the ETL should backup NIfTI files.
  • For SUBJECT_ID_MAPPING_PATH, specify the path to the CSV file containing subject ID mappings.

Next, run update to build the container image and initialize the database:

$ ./scripts/update

Finally, use console to enter a shell environment within the container that contains all the CLI's dependencies:

$ ./scripts/console

And, voilà, the CLI should fully functional ✨:

$ image-deid-etl -h
usage: image-deid-etl [-h] [--program [{cbtn,corsica}]] [--site [SITE]] {initdb,importuuids,check,validate,run,upload2fw,add-fw-metadata,s3-backup-niftis} ...

A WIP tool to assist with reading DICOM images from Orthanc, conversion to anonymized NIfTI images, and uploading to Flywheel.

positional arguments:
  {initdb,importuuids,check,validate,run,upload2fw,add-fw-metadata,s3-backup-niftis}
    validate            check sub/ses mapping
    run                 download images and run deidentification
    upload2fw           upload results to Flywheel, when complete
    add-fw-metadata     add metadata in JSON sidecars to NIfTIs on Flywheel
    s3-backup-niftis    copies NIfTIs to S3

optional arguments:
  -h, --help            show this help message and exit
  --program [{cbtn,corsica}]
                        program namespace (default: cbtn)
  --site [SITE]         site namespace (default: chop)

Example Usage

To check Orthanc for and process N number of new studies, pipe the output of check into the run command:

$ image-deid-etl check --limit N --raw | xargs image-deid-etl run

To process an individual study, specify an Orthanc UUID after the run command:

$ image-deid-etl run UUID

Development

AWS

CHOP's AWS SSO configuration will automatically sign you out of your session every 1 to 2 hours. If you encounter any permission errors, your session has likely expired. Follow these instructions to refresh your login, using the aws sso login command.

If you do not have the AWS CLI v2 installed locally, you will need to execute these steps from within the container image.