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This page has not been upda= ted since 2014 and is no longer being maintained. Please visit= http://mir= cwiki.rsna.org/index.php?title=3DCTP-The_RSNA_Clinical_Trial_Processor&= nbsp;for the most up to date CTP documentation.
The purpose of this page is to serve as a beginner's guide to Clinical T= rials Processor (CTP) with particular emphasis on internal de-identificatio= n of DICOM images and submission of this data to an instance of NBIA or XNA= T. If you are already familiar with how CTP works and just want help with c= onfiguring it please proceed to the Example CTP use cases and configuration fil= es page.
Note: This page is currently a work in progress. Thi= s note will be removed once documentation is considered mostly complete.
The basic outline of steps required to utilize CTP include:
Each step is described in detail below. At the end of the page there is = also a section with customized configuration files and scripts for the most= common CTP use cases.
It's possible you may not actually need to install anything prior to usi= ng CTP and there are only 2 potential things you may need to obtain prior t= o using CTP:
CTP can be found in 2 locations. Generally the two packages stay reasona= bly close together in terms of functionality. If you are looking for a new = feature that you've heard about in CTP use the RSNA link. If you're just lo= oking for a stable way to de-identify your data or if you need to submit de= -identified data to NBIA use the GForge link.:
Once you have downloaded CTP you will need to extract it to a location o= n your local hard drive. The method for doing this varies by operating syst= em and the installer you chose to download.
Once you've installed CTP you must setup some configuration options prio= r to running it. All of these options are specified with the config= .xml file located in the root of the CTP installation directory. T= his can be easily modified using any text editor and is divided into severa= l "pipeline stages" for importing, processing, and exporting your data. The= rest of this section explains the basic structure of the config.xm= l file.
An example below describes a customized config.xml file is shown below. = The pipeline described by this script will receive DICOM data on port 24104= , anonymize them using the script and lookup table you can specify, and sav= e the anonymized data in the specified root. Script, lookup table and root = are marked in the script.
<Con= figuration> <Server port=3D"24080"/> <Pipeline name=3D"Main Pipeline"> <ImportService=20 name=3D"dicomImport" id=3D"dicomImport" class=3D"org.rsna.ctp.stdstages.DicomImportService" root=3D"roots/dicomImportService"=20 port=3D"24104"=20 logConnections=3D"no" suppressDuplicates=3D"no" /> =20 <Processor name=3D"pixel-checker" id=3D"pixel-checker" class=3D"org.rsna.ctp.stdstages.DicomFilter" root=3D"roots/pixel-checker"=20 script=3D"scripts/pixel-checker-filter.script" quarantine=3D"quarantines/pixel-checker" /> =20 <Processor name=3D"idmap" class=3D"org.rsna.ctp.stdstages.IDMap" root=3D"roots/idmap" /> <StorageService name=3D"storage" id=3D"storage" class=3D"org.rsna.ctp.stdstages.FileStorageService" root=3D"/projects/qin/CTPStorageDir" <!= -- ROOT: CUSTOMIZE THIS! --!> type=3D"month" timeDepth=3D"0" acceptDuplicateUIDs=3D"yes" acceptDicomObjects=3D"yes" acceptXmlObjects=3D"no" acceptZipObjects=3D"no" acceptFileObjects=3D"no"=20 returnStoredFile=3D"yes" quarantine=3D"quarantines/storage" /> =20 <Anonymizer name=3D"DicomAnonymizer" class=3D"org.rsna.ctp.stdstages.DicomAnonymizer" root=3D"de-id/dicom-anonymizer" script=3D"scripts/QIN-PROSTATE-BWH.script" <!-= - SCRIPT: CUSTOMIZE THIS! --!> lookupTable=3D"scripts/bwh_deid_list_internal.txt" <!= -- LOOKUP TABLE: CUSTOMIZE THIS! --!> quarantine=3D"quarantines/dicom-anonymizer" /> </Pipeline> </Configuration>
Anonymizer script defines the rules for DICOM anonymization. You can use= the default CIP CTP script available here: https://wiki.nci.nih.gov/download/attachments/39295860/ctp-s142-cleaner.s= cript as the starting point for customization. This script allows you t= o choose which tags you would like to keep/remove/change, and allows you to= offset the dates.
Lookup table is optional, and when specified, it allows to map the origi= nal IDs to the anonymized patient IDs. The format of this file is the follo= wing:
ptid/OR= IGINAL_SUBJECT_ID=3DDEIDENTIFIED_SUBJECT_ID
Once you configured the import pipeline, you can launch CTP service usin= g the launcher located in the installation directory =E2=80=93 see the dire= ctions on running CTP here: http://mircwiki.rsna.org/index.php?title=3DCTP-The_= RSNA_Clinical_Trial_Processor#Running_CTP You should use the web inte= rface of CTP to monitor the progress of transmission. You can also use it t= o change your deidentification script, check the mapping of subject IDs, an= d shutdown the CTP service once the transmission is finished.
There are 3 primary locations which you can import data from with CTP.= p>
The RSNA site's documentation contains detailed information on customi= zing CTP based on your incoming data source
You can use the utility FileSender http:=
//mircwiki.rsna.org/index.php?title=3DFileSender
CTP contains a number of specialized processing "pipelines" for modifyin= g the contents of your data. Again the RSNA wiki site explains all of the <= a href=3D"http://mircwiki.rsna.org/index.php?title=3DCTP-The_RSNA_Clinical_= Trial_Processor#Processors" class=3D"external-link" rel=3D"nofollow">CTP Pr= ocessors in full detail, but below you will find a list of the most c= ommon types of processing pipelines and a short summary of their function:<= /p>
The most common ways of exporting the data which you've processed in CTP= include:
Full details relating to how each of these can be customized along with = the other export methods can be found on the RSNA wiki in the Export Servic= es section and the Storage Service section respectively.