Name: mirc-ctp
Owner: Stanford School of Medicine
Description: Stanford IRT/RIT base DICOM anonymization scripts. READ DISCLAIMER.
Created: 2018-02-12 22:57:10.0
Updated: 2018-03-20 22:58:52.0
Pushed: 2018-02-13 01:07:39.0
Size: 29
Language: Shell
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DISCLAIMER: These anonymization scripts are only provided for testing the MIRC-CTP DICOM file output with your application. They are not intended to be used in a clinical or research setting, and should be considered incomplete test samples. DICOM files filtered through this program and associated scripts are not guaranteed to be free of PHI.
This project contains baseline MIRC-CTP de-identification and filtering scripts used within Stanford IRT-RIT for anonymizing DICOM studies at scale. Use these scripts to verify that the Stanford IRT-RIT de-identification pipeline produces output acceptable for your study.
Included in this project is the MIRC-CTP command-line DicomAnonymizerTool which allows de-identification of DICOM studies without installing the entire MIRC-CTP application. The Stanford IRT-RIT anonymization pipeline uses this same library.
stanford-anonymizer.script: This file specifies which DICOM tags should be modified or removed.stanford-filter.script: This file specifies which DICOM instances should be removed. Currently includes image types known to have pixel data with PHI, for example secondary derived screens (screenshots).The anonymization scripts are based off the DICOM-PS3.15E-Basic profile with additional rules for tags known to contain PHI. All vendor-specific (eg. odd-numbered) tags are also removed.
First ensure you have the Oracle JDK v.8 installed.
Create a clone of this repository on your workstation:
clone --recurse-submodules https://github.com/susom/mirc-ctp.git
If you do not have the ant program installed, install it with HomeBrew (which will need to be installed if you haven't done so already)
ew install ant
Compile the included DicomAnonymizerTool by typing ant at the command prompt:
t
dfile: /Users/jdoe/Projects/mirc-ctp/build.xml
n:
:
[echo] Time now 15:56:40 PST
[echo] ant.java.version = 1.8
[mkdir] Created dir: /Users/jdoe/Projects/mirc-ctp/DicomAnonymizerTool/build
You should now have a directory called DAT which contains the DicomAnonymizerTool. You can try running it:
va -jar DAT/DAT.jar
e: java -jar DAT {parameters}
e:
n {input} specifies the file or directory to be anonymized
If {input} is a directory, all files in it and its subdirectories are processed.
ut {output} specifies the file or directory in which to store the anonymized file or files.
You can now place some test DICOM studies in the directory DICOM and run the shell script which will anonymize the studies (all to the same anonymous MRN and Accession Number) and place them in DICOM-ANON
anonymize.sh
ad: pool-1-thread-1: Anonymizing DICOM/1.2.840.4267.32.293501795892579834759834759834759834
nonymized file: DICOM-ANON/1.2.840.4267.32.10027221686667529588514012002002498656
ad: pool-1-thread-2: Anonymizing DICOM/1.2.840.4267.32.093248509348509384509384509834059840
nonymized file: DICOM-ANON/1.2.840.4267.32.10134745174550989356450666756661275833
sed time: 0.634
You can now open the DICOM files in DICOM-ANON to make sure they work with your intended application.
You may want to look at the contents of anonymize.sh to understand how the MIRC-CTP application is invoked.