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Mission

Mark Anderson at Surgical Planning and Channing labs currently manages data for many investigators, pulling data from PACS into the research environment. There is interest in setting up a parallel channel by which the data are also enrolled into an XNAT database and accessed from client, and comparing its ease of use with the existing infrastucture. To explore XNAT as a possible long-term informatics solution for the NCIGT project, Mark will be uploading retrospective data for a number of NCIGT efforts (and PIs):

NCIGT_Brain_Function (SS/AG)
- Key Investigators:
- Brief Description:
NCIGT_Tumor_Resection (HK/AG)
- Key Investigators:
- Brief Description:
NCIGT_Prostate (HE/CT)
- Key Investigators:
- Brief Description:
NCIGT_Prostate_Fully_Segmented (HE/CT)
- Key Investigators:
- Brief Description:
NCIGT_Brain_Biopsy (FT)
- Key Investigators:
- Brief Description:

Use-Case Goals

Step 1. Data Management

Anonymize, apply DICOM metadata and upload retrospective datasets; confirm appropriate organization and naming scheme via web GUI.

Step 2. Query & Retrieval

Make specific queries using XNAT web services,
Download data conforming to specific naming convention and directory structure, using XNAT web services

Each effort listed above will have different requirements for being able to query, retrieve and use data collections. Brief description of how retrospective data will be used within the NCIGT is described below:

NCIGT_Brain_Function:
NCIGT_Tumor_Resection:
NCIGT_Prostate:
NCIGT_Prostate_Fully_Segmented:
NCIGT_Brain_Biopsy:

Step 3. Disseminating & Sharing

In addition to NCIGT mandate to share data, each effort listed above will have different requirements for being able to make data available to collaborating and other interested groups.

Outcome Metrics

Step 1. Data Management

Step 2. Query & Retrieval

Step 3. Dissemination & Sharing

Fundamental Requirements

Participants

Mark Anderson
Tina Kapur

Data

Workflows

Current Data Management Process

Target Data Management Process (Step 1.) Option A.

Create new project using web GUI
Manage project using web GUI: Configure settings to automatically place data into the archive (no pre-archive)
Create a subject template (download from web GUI)
Create a spreadsheet conforming to subject template
Upload spreadsheet using web GUI to create subjects
Run CLI Tool for batch anonymization (See here for HowTo: http://nrg.wustl.edu/projects/DICOM/DicomBrowser/batch-anon.html)
Need pointer for script to do batch upload & apply DICOM metadata.
Confirm data is uploaded & represented properly with web GUI

Target Data Management Process (Step 1.) Option B. (web services API) CURRENTLY BEING TESTED!

1. Create new project on XNAT instance using web GUI

Manage project using web GUI: Configure settings to automatically place data into the archive (no pre-archive)

2. Batch Anonymize

The approach to writing anonymization scripts is here: http://nrg.wustl.edu/projects/DICOM/AnonScript.jsp
See description for batch anonymization here: http://nrg.wustl.edu/projects/DICOM/DicomBrowser/batch-anon.html
Download and install commandline tools: http://nrg.wustl.edu/projects/DICOM/DicomBrowser-cli.html

2.a Create a remapping config xml file to describe the spreadsheet to be built from the DICOM data. Root element is "Columns" and each subelement describes a column in the spreadsheet:

tag = DICOM tag
level = (global, patient, study, series) describes the level at which the remapping is applied

An example is:

<Columns>
 <Global remap="Fixed Institution Name">(0008,0080)</Global>
 <Global remap="Anon Requesting Physician" (0032,1032)</Global>
 <Patient remap="Anon Patient Name">(0010,0010)</Patient>
 <Patient remap="Anon PatientID">(0010,0020)</Patient> 
 <Patient remap="Anon Patient Address" (0010,1040)</Patient>
 <Study>(0020,0010)</Study>
 <Study>(0008,0020)</Study>
 <Series>(0020,0011)</Series>
 <Series>(0008,0031)</Series>
</Columns>

2.b Generate a spreadsheed from the data:

  DicomSummarize -c remap-config-file.xml -v remap.csv [directory-1 ...]

where the arguments in brackets are a list of directories containing the source DICOM data (separated by spaces?)

2.c Write an anonymization script for any simple changes, such as deleting an attribute, or setting an attribute value to either a fixed value or a simple function of other attribute values in the same file. The more changes you can put into this anonymization script, the simpler will be the rest of this process.

See http://nrg.wustl.edu/projects/DICOM/AnonScript.jsp for detailed information about writing anonymization scripts. Here's a script written by Mark during his testing.

// removes all attributes specified in the
//  DICOM Basic Application Level Confidentiality Profile
// mark@bwh.harvard.edu added the following tags:
// (0010,1040) PatientsAddress
// (0032,1032) RequestingPhysician
// is seems the study and series InstanceUID tags are needed  (0020,000D) (0020,000E)
//- (0020,000D)
//- (0020,000E)
// - (0010,1010) preserve pt age
// - (0010,1040) preserve pt sex
- (0008,0014) 
- (0008,0050)
- (0008,0080)
- (0008,0081)
- (0008,0090)
- (0008,0092)
- (0008,0094)
- (0008,1010)
 (0008,1030) := "SPL_IGT"
- (0008,1040)
- (0008,1048)
- (0008,1050)
- (0008,1060)
- (0008,1070)
- (0008,1080)
- (0008,2111)
 (0010,0010) := "case143"
 (0010,0020) := "case143"
- (0010,0030)
- (0010,0032)
- (0010,1040)
- (0010,0040)
- (0010,1000)
- (0010,1001)
- (0010,1020)
- (0010,1030)
- (0010,1090)
- (0010,2160)
- (0010,2180)
- (0010,21B0)
- (0010,4000)
- (0018,1000)
- (0018,1030)
 (0020,0010) := "MR1"
- (0020,0052)
- (0020,0200)
- (0020,4000)
- (0032,1032)
- (0040,0275)
- (0040,A124)
- (0040,A730)
- (0088,0140)
- (3006,0024)
- (3006,00C2)

NOTE DicomBrowser doesn't write directly into the database -- it can send to a DICOM server.

2.d Edit the spreadsheet (remap.csv file) that is generated as output.

This spreadsheet will contain all the columns you defined, plus some additional columns needed to uniquely identify each patient, study, and series.

Each new (remap) column should be filled with values. In some cases, some cells in the spreadsheet can be left blank: for a Patient-level remap, one value must be specified for each patient; if the spreadsheet contains multiple rows for each patient, the column needs only be filled in one row for each patient. Similarly, for a Study-level remap, the value need only be filled once. If you don't fill in a required cell, the remapper will complain. If you give, for example, a Patient-level remap column multiple values for a single patient, the remapper will complain.

2.e Run the remapper:

DicomRemapper -c remap-config-file.xml -o <path-to-output-directory> -v remap.csv [directory-1 ...]

the remap config XML should be the same file used in 2.a,
remap.csv is the spreadsheet generated in 2.c and edited in 2.d, and
list of directories is the same list of source directories from 2.e.
add an anonymization script to be applied at this stage by using the -d option.
first time you use a script to generate new UIDs, you'll need a new UID root;
- do this by adding -s http://nrg.wustl.edu/UIDGen to the DicomRemapper command line.

For next steps using web services, use curl or XNATRestClient (See here to download XNATRestClient in xnat_tools.zip from here: http://nrg.wikispaces.com/XNAT+REST+API+Usage)

3. Authenticate with server and create new session; use the response as a sessionID ($JSessionID) to use in subsequent queries

curl -d POST $XNE_Svr/REST/JSESSION -u $XNE_UserName:$XNE_Password 
or, use the XNATRestClient
XNATRestClient -host $XNE_Svr -u $XNE_UserName -p $XNE_Password -m POST -remote /REST/JSESSION

4. Create subject

 XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT /REST/projects/$ProjectID/subjects/s0001 
(This will create a subject called 'S0001' within the project $ProjectID)

A script can be written to automatically create all subjects for the project.

4a. specify the demographics of a subject already created, or create with demographic specification

4.a.1 No demographics are applied to each subject by default. To edit the demographics (like gender or handedness) of a subject already created using XML Path shortcuts.

xnat:subjectData/demographics[@xsi:type=xnat:demographicData]/gender = male
xnat:subjectData/demographics[@xsi:type=xnat:demographicData]/handedness = left

The entire command looks like this (Append XML path shortcuts and separate each by an &. Note that querystring parameters must be separated from the actual URI by a ?):

XNATRestClient -host $XNE_svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/s0001?xnat:subjectData/demographics[@xsi:type=xnat:demographicData]/gender=male&xnat:subjectData/demographics[@xsi:type=xnat:demographicData]/handedness=left"

All XML Path shortcuts that can be specified on commandline for projects, subject, experiments are listed here: http://nrg.wikispaces.com/XNAT+REST+XML+Path+Shortcuts

4.a.2 Alternatively, specify the demographics during subject creation by generating and uploading an xml file with the subject:

XNATRestClient -host $XNE_srv -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/s0002" - local ./$ProjectID_s0002.xml

The XML file you create and post looks like this:

<xnat:Subject ID="s0002" project="$ProjectID" group="control" label="1" src="12"  xmlns:xnat="http://nrg.wustl.edu/xnat" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
   <xnat:demographics xsi:type="xnat:demographicData">
       <xnat:dob>1990-09-08</xnat:dob>
       <xnat:gender>female</xnat:gender>
       <xnat:handedness>right</xnat:handedness>
       <xnat:education>12</xnat:education>
       <xnat:race>12</xnat:race>
       <xnat:ethnicity>12</xnat:ethnicity>
       <xnat:weight>12.0</xnat:weight>
       <xnat:height>12.0</xnat:height>
   </xnat:demographics>
</xnat:Subject>

4.b (optional check) Query the server to see what subjects have been created:

XNATRestClient -host $XNE_Svr -user_session $JSessionID -m GET -remote /REST/projects/$ProjectID/subjects

4.c Create experiments (collections of image data) you'd like to have for each subject

XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/MRExperiment?xnat:mrSessionData/date=01/02/09"
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/CTExperiment1?xnat:ctSessionData/date=01/02/09"
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/PETExperiment1?xnat:petSessionData/date=01/02/09"

4.d (optional check) Query the server to see what experiments have been created:

XNATRestClient -host $XNE_Svr -user_session $JSessionID -m GET -remote /REST/projects/$ProjectID/subjects/s0001/experiments?format=xml

5. Batch Anonymize scan data

Run CLI Tool for batch anonymization (See here for HowTo: http://nrg.wustl.edu/projects/DICOM/DicomBrowser/batch-anon.html)

Also See here for new (possibly buggy) command line options: http://nrg.wustl.edu/projects/DICOM/DicomBrowser-cli.html

6. Create metadata from DICOM headers

7. Create uris for scans, reconstructions and upload them.

Note: when uploading images, it is good form to define the format of the images (DICOM, ANALYZE, etc) and the content type of the data. This will not translate any information in the DICOM header into metadata on the scan.

//create SCAN1
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/scans/SCAN1?xnat:mrScanData/type=T1"

/upload SCAN1 files...
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/scans/SCAN1/files/1232132.dcm?format=DICOM&content=T1_RAW" -local /data/subject1/session1/RAW/SCAN1/1232132.dcm


//create SCAN2
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/scans/SCAN2?xnat:mrScanData/type=T2"

//upload SCAN2 files...
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/scans/SCAN2/files/1232133.dcm?format=DICOM&content=T2_RAW" -local /data/subject1/session1/RAW/SCAN2/1232133.dcm


//create reconstruction 1
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/reconstructions/session1_recon_0343?xnat:reconstructedImageData/type=T1_RECON"

//upload reconstruction 1 files...
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/reconstructions/session1_recon_0343/files/0343.nfti?format=NIFTI" -local /data/subject1/session1/RECON/T1_0343/0343.nfti


//create reconstruction 2
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/reconstructions/session1_recon_0344?xnat:reconstructedImageData/type=T2_RECON"

//upload reconstruction 2 files...
XNATRestClient -host $XNE_Svr -user_session $JSessionID -m PUT -remote "/REST/projects/$ProjectID/subjects/$SubjectID/experiments/$ExperimentID/reconstructions/session1_recon_0344/files/0344.nfti?format=NIFTI" -local /data/subject1/session1/RECON/T1_0344/0344.nfti

8. Confirm data is uploaded & represented properly with web GUI

CTSC IGT, BWH

Contents

Mission

Use-Case Goals

Outcome Metrics

Fundamental Requirements

Participants

Data

Workflows

Current Data Management Process

Target Data Management Process (Step 1.) Option A.

Target Data Management Process (Step 1.) Option B. (web services API) CURRENTLY BEING TESTED!

Target Query Formulation (Step 2.)

Target Processing Workflow (Step 3.)

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