> ## Documentation Index > Fetch the complete documentation index at: https://docs.encord.com/llms.txt > Use this file to discover all available pages before exploring further. # De-identifying DICOM Files DICOM files may contain sensitive and personally identifiable information (PII) about patients, including their name, date of birth, medical record number. In these cases it is essential to anonymize each file, to protect patient privacy and comply with legal and ethical regulations related to healthcare data. This is a premium feature and running it incurs additional costs. Contact us at [support@encord.com](mailto:support@encord.com) to learn about pricing. In this tutorial you will learn how to anonymize / de-identify DICOM files in two steps: 1. [Setting up the de-identification function](#set-up-the-de-identification-function). 2. [Using the de-identification function](#de-identifying). Finally, you will learn how to [interpret the JSON output](#output) of the de-identification process. Redacted tag values are completely removed. ## Set up the de-identification function Adjust the de-identification function [found here](/sdk-documentation/sdk-references/user_client#deidentify_dicom_files) to suit your needs. ## De-identifying The Python code below is used to add criteria and call the de-identification function. An SSH public / private key pair is required to use the sample script below. To learn how to generate one, see our documentation [here](/platform-documentation/General/general-access-keys). Make sure to edit the `criteria` used to evaluate each file to suit your needs - any number of criteria can be used. ```python theme={"dark"} import multiprocessing import time from pathlib import Path from typing import List import glob import os from encord import EncordUserClient from encord.objects.common import ( DeidentifyRedactTextMode, SaveDeidentifiedDicomConditionNotSubstr, SaveDeidentifiedDicomConditionIn ) # Replace s3://EXAMPLE-BUCKET/raw/ with the path to the file storage you're using def filelist_helper(dir,prefix='s3://EXAMPLE-BUCKET/raw/'): fl = [prefix+os.path.basename(f) for f in glob.glob(dir+"*.dcm")] return fl # Add criteria to evaluate each file. See the 'Setting evaluation criteria' section below for more info. criteria = [ SaveDeidentifiedDicomConditionNotSubstr("PRIMARY","ImageType"), SaveDeidentifiedDicomConditionIn(["ct","pt","nm","mr","mg","pt"],"Modality") ] def deidentify( integration_title: str, dicom_urls: List[str], ) -> List[str]: # Authenticate with Encord using the path to your private key user_client = EncordUserClient.create_with_ssh_private_key(ssh_private_key_path="") integration_hash = None # Find integration_hash for requested integration_title for integration in user_client.get_cloud_integrations(): if integration.title == integration_title: integration_hash = integration.id if not integration_hash: raise Exception(f"Integration with integration_title={integration_title} not found") deidentified_dicom_urls = [] # 'dicom_urls' should be a a single list containing the URLs of all instances of a series to be de-identified. Splitting a series into multiple lists might lead to inaccurate results and is therefore not recommended deidentified_dicom_url = user_client.deidentify_dicom_files( dicom_urls=dicom_urls, integration_hash=integration_hash, redact_dicom_tags = True, redact_pixels_mode = DeidentifyRedactTextMode.REDACT_ALL_TEXT, save_conditions = criteria, upload_dir = "s3://EXAMPLE-BUCKETt/output" ) print(f"Deidentified url: {deidentified_dicom_url}") deidentified_dicom_urls += deidentified_dicom_url return deidentified_dicom_urls # Replace MY-ENCORD-INTEGRATION with the title of your private cloud integration _integration_title = "MY-ENCORD-INTEGRATION" _deidentified_dicom_urls = deidentify( _integration_title, _dicom_urls, ) ``` ### Setting evaluation criteria Evaluation criteria are conditions that determine whether a file will be de-identified or not. Criteria can take many forms, but will always return either 'true' or 'false'. All strings and inputs into the criteria functions are case-insensitive. There are two distinct criteria functions: * "SaveDeidentifiedDicomConditionNotSubstr" will return 'true' if the first argument (PRIMARY in the example above), is not contained in the second argument (ImageType in the example above). In plain English, the example above checks whether the file's ImageType doesn't contain the word 'Primary', and returns 'true' if this condition is fulfilled. * "SaveDeidentifiedDicomConditionIn" will return 'true' if the first argument (\["ct","pt","nm","mr","mg","pt"] in the example above) is contained in the second argument Modality. In plain English, the example above checks whether any of the strings contained in the list are contained within the file's Modality. If any one of them is, the function returns 'true'. ## Output This section will explain the output of the de-identification function. Click the dropdown below to see a sample output file ```json theme={"dark"} { "url": "s3://EXAMPLE-BUCKETt/raw/should_fail_1.2.840.113619.2.283.6945.3146400.16119.1391477777.833.dcm", "StudyInstanceUID": "1.2.840.113619.6.283.4.679947340.8065.1391798290.307", "StudyInstanceUID_deid": "1.2.840.113619.6.283.4.679947340.8065.1391798290.307", "SeriesInstanceUID": "1.2.840.113619.2.283.6945.3146400.21673.1391477673.97", "SeriesInstanceUID_deid": "1.2.840.113619.2.283.6945.3146400.21673.1391477673.97", "save_conditions_evaluations": [ { "condition": { "value": "PRIMARY", "condition_type": "NOT_SUBSTR", "dicom_tag": "ImageType" }, "tag_value": "DEMOGRAPHICDATA", "evaluated_value": false }, { "condition": { "value": [ "ct", "pt", "nm", "mr", "xr", "mg" ], "condition_type": "IN", "dicom_tag": "Modality" }, "tag_value": "MR", "evaluated_value": true } ], "save_condition": false, "save_condition_series_agg": false, "save_disabling_urls_series_agg": [ "s3://EXAMPLE-BUCKETt/raw/should_fail_1.2.840.113619.2.283.6945.3146400.16119.1391477777.833.dcm" ], "url_deid": "s3://EXAMPLE-BUCKETt/Pixel-redaction-ready/deid_169089614143326592_should_fail_1.2.840.113619.2.283.6945.3146400.16119.1391477777.833.dcm" } ``` | **Key** | **Description** | **Notes** | | -------------------------------- | -------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | | `url` | A URL to the DICOM file | | | `StudyInstanceUID` | The study's ID | | | `StudyInstanceUID_deid` | A converted version of the study's ID used by Encord | Identical to `StudyInstanceUID`, unless `StudyInstanceUID` was invalid | | `SeriesInstanceUID` | The series' ID | | | `SeriesInstanceUID_deid` | A converted version of the series' ID used by Encord | Identical to `SeriesInstanceUID`, unless `SeriesInstanceUID` was invalid | | `save_conditions_evaluations` | Contains a list of conditions | These need to be met in order for a file to be de-identified | | `condition` | Contains a given condition's details | A `condition` is satisfied when the `value` fulfills the `condition_type` | | `value` | The elements being evaluated by the `condition_type` | Can be thought of as the 'answer' to a `condition` | | `condition_type` | The type of condition being evaluated | Can be thought of as the 'question' to a `condition` | | `dicom_tag` | The DICOM tag on which a condition is being evaluated | | | `save_condition` | Does the condition have to be `true` or `false` for the file to pass | | | `save_condition_series_agg` | The series as a whole evaluated as `true` or `false` | For this to be `true` **all** `save_condition`s need to be `true` For this to be `false` **all** `save_conditions`s need to be `false` | | `save_disabling_urls_series_agg` | A list of files which did not meet the required `save_condition` | Only relevant if the series didn't pass | | `url_deid` | The URL of the new, de-identified file. | |