De-idenfication Profiles

De-identification profiles define which fields mrscrub should modify and how. These profiles should be written in YAML.

Overview

The general structure of a de-identification profile is

dicom:
  fields:
    - name: FieldName
      tag:
      - hex group code
      - hex element code
      action:
        action-name: value

Here’s a quick overview of what we’re looking at

• dicom

  • fields: a list of fields to de-identify

    • name: a name for the field (your choice)

    • tag: a DICOM tag (2 hex values)

    • action

      • action-name: the action you want to apply

Actions

There are several actions you can apply to any DICOM field.

replace-with

If you want your de-identification policy to replace PatientName (0010,0010) with a new string (or an empty string ''), you can use the replace-with action

dicom:
  fields:
    - name: PatientName
      tag:
      - 0x0010
      - 0x0010
      action:
        replace-with: 'a new string'

By default, no action is performed if the targeted DICOM tag doesn’t exist. However, if you’d like to create the missing tag before assignining the replacement value, you can add create: true

dicom:
  fields:
    - name: PatientName
      tag:
      - 0x0010
      - 0x0010
      action:
        replace-with: 'a new string'
        create: true

new-uid

Removing dates is doable using replace-with, but UIDs within a DICOM data set can also contain dates. To reassign SOPInstanceUID (0008,0018) for example, you can use the new-uid action

dicom:
  fields
    - name: SOPInstanceUID
      tag:
      - 0x0008
      - 0x0018
      action:
        new-uid: true

Note

Note that replacing SOPInstanceUID will also trigger the replacement of any ReferencedSOPInstanceUID instances within SourceImageSequence or ReferencedImageSequence.

delete

Sometimes you may want to delete a field entirely. For example, to delete the Siemens CSA header (0029,1020), you can use the delete action

dicom:
  fields
    - name: Unknown
      tag:
      - 0x0029
      - 0x1020
      action:
        delete: true

Templating

scrub.py can find and replace template strings within your de-identification profile before the profile is applied to your data set.

Note

Template strings must be surrounded by curly braces {...}

Let’s assume you want to add the text Project:MyProjectName to the PatientComments (0010,4000) field for every DICOM file in your data set. However, you know beforehand that different data sets may need different project names. You could maintain a separate copy of your de-identification profile for each project name, or use template strings

dicom:
  fields
    - name: StudyComments
        tag:
        - 0x0010
        - 0x4000
        action:
            replace-with: Project:{project}

If your de-identification profile contains template strings, you can use scrub.py --replace to replace those strings with a custom value

scrub.py --replace project=MyProjectName

You can use any number of template strings within your de-identification profile and provide the corresponding key/value pair to --replace, each one separated by a single space

scub.py --replace key1=value1 key2=value2 key3=value3

Example

You can find an example de-identification profile here.