using the cnda

Using the CNDA

Dan Marcus & CNDA StaffJuly 11, 2014

QUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESS

IMAGING

METADATA

OTHER SOURCES

What is the CNDA?

• Data archiving• Quality control• Data access• Security

• Visualization• Automation• Integration• Data sharing

History of the CNDA2002: Initiated to manage ADRC Imaging Core data.2004: Expanded to include additional studies of aging.2005: XNAT spun off as open source data management

platform.2006: NRG moved to Mallinckrodt and CNDA made

widely available to Wash U imaging community.2013: All CCIR data archived to CNDA.2014: All East Building MR Facility data archived to CNDA.

The CNDA Today

• > 400 active users• > 1,100 registered projects• > 32,000 subjects• > 49,000 sessions• > 50 TB total storage

Security

• Project access can be set to private, public, or protected.

• Projects are private by default.• Project access is controlled by study PI or

designee.• Users are assigned roles on projects to

configure their level of access (owner, member, collaborator).

Image Upload: CCIR

• CNDA projects are created by Betsy Thomas from study registration paperwork (no longer need to “opt-in”).

• CCIR protocol # (e.g. CCIR-1234) is assigned as CNDA project ID.

• PI & listed personnel are added to project.• Scans are sent to CNDA by scanner techs.• CCIR protocol # is embedded in DICOM tag

((0008,1030) Study Description).• CNDA uses protocol # in DICOM to route data to

correct project.

Image Upload: East Building MR Facility

• CNDA projects are created automatically by RIIS during study registration.

• RIIS protocol number (“NP123”) is assigned as CNDA project ID.

• All study personnel listed in RIIS are added to CNDA project.

• Scans are sent automatically by scanner to CNDA.• CNDA communicates with RIIS to route data to

correct project.

Image Upload: DICOM mappingsDICOM Field CNDA Field

(0008,1030) Study Description OR(0008,0050) Accession Number

Project

(0010,0010) Patient's Name Subject Label

(0010,0020) Patient ID Session Label

(0020,0011) Series Number Scan Number

(0008,103E) Series Description Series Description

(0010,4000) Patient Comments OR(0032,4000) Study Comments

Comma-separated list of project, subject, session

(0008,1030) Study Description OR(0008,0050) Accession Number (0010,0010) Patient's

Name

(0010,0020) Patient ID

Image Upload: Remote Sites

• Caution: DICOM network protocol is NOT (usually) encrypted.

• Caution: DICOM data may include PHI.• Therefore: Do NOT send directly from scanner.

Option 1: Web uploader


Option 1: Web Uploader• Entirely web-based – no installation required.• Automatically removes PHI from DICOM files.• Wizard-style interface automatically assigns

data to project, subject, session.• Allows user to review files before sending.• Best option for occasional uploads from a site.


Option 2: CTP Relay• Requires hardware installation &

network configuration.• Automatically removes PHI from

DICOM files.• Automatically transfers data.• Project, subject, & session IDs

must be entered in DICOM fields.• Best option for frequent uploads

from a site.

Image Upload: Clinical Scans

• DICOM data will definitely include PHI.• Scans can not be sent directly from clinical

scanners to CNDA.• Pulling data from clinical PACS is difficult.• Retrospective studies often require 100s or

1000s of scans.

Image Upload: Clinical Scans

Option 1: “JAAT”• Send spreadsheet to

CNDA staff.• JAAT retrieves scans

from PACS, anonymizes, and uploads to CNDA.

• Hospital throttles requests so retrieval can take several days.

• Best option for large batches of data

Image Upload: Clinical ScansOption 2: Web Uploader• Entirely web-based – no

installation required.• Automatically removes PHI from

DICOM files.• Wizard-style interface

automatically assigns data to project, subject, session.

• Allows user to review files before sending.

• Need to obtain scans on your own.• Best option for default

anonymization.

Image Upload: Clinical ScansOption 3: DICOM Browser• Desktop application allows

viewing DICOM data.• Manually edit DICOM

metadata.• Apply custom DICOM edit

scripts.• Send over DICOM protocol

to CNDA.• Best option for custom

anonymization.http://nrg.wustl.edu/software/dicom-browser

Image Upload: Clinical ScansOption 4: Direct retrieval from PACS*• Enter patient information

into web form.• Study is anonymized and

imported to CNDA in real-time.

• Already implemented on TIP.

• Best option for quick single study retrieval.

* Coming to CNDA soon (Fall-ish)

Data Storage Costs

• CCIR Scans: No charge• East Building MR Facility: No charge• Remote Sites:• Clinical Scans: $5/imaging session• Bulk Upload: $5/imaging session• Remote Data: $10/imaging session• Extra storage on NRG’s ZFS system: $750/TB

Details @ http://cnda-help.wustl.edu/CNDA+Rates

Accessing Data: Web download

Accessing Data: File System

• Obtain nrg login & VPN access (contact [email protected]).

• Request read access to your project directory.• Access on nrg cluster:

– ssh [email protected]– cd /data/CNDA/archive/CONDR_METS

• Mount on local computer:– sshfs

[email protected]:/data/CNDA/archive/CONDR_METS . -o defer_permissions -o volname=CONDR_METS

mailto:[email protected]

Accessing Data: File System

Accessing Data: Scripts

• CNDA includes a “RESTful” programming interface.• All CNDA objects can be accessed through a

controlled set of URLs.• Use this programming interface to write scripts to

interact with CNDA• Some helper tools: curl, pyxnat, XNAT Data Client• Details at

https://wiki.xnat.org/display/XNAT16/Using+the+XNAT+REST+API

Accessing Data: XNAT Gateway

Modality Workstation

CNDA



CNDA

DICOM?DICOM



CNDA

DICOM?DICOMHTTPS



CNDA

DICOM?DICOMHTTPS

XNAT Gateway: DICOM adapter


https://wiki.xnat.org/display/XNAT/XNAT+Gateway+Server+User+Manual


https://wiki.xnat.org/display/XNAT16/XNAT+Gateway+Setup+for+Osirix

Image Processing Pipelines

• CNDA includes pipelines for standard neuroimaging processing and analysis– format conversion– atlas registration– BOLD and rs-fMRI processing– Etc.

• Details @ http://cnda-help.wustl.edu/CNDA+Pipelines+Overview

• Custom pipelines can be developed.

Image Processing Pipelines

Non-imaging Data

Option 1: Custom Variables• Do it yourself from

project page.• Appear on data edit

screens.• Best option for

small extensions.

Non-imaging Data

Option 2: Schema Extensions• Requires CNDA staff

to generate.• CNDA creates

database tables, forms, etc.

• Best option for formal extensions.

Non-imaging Data

Option 2: Schema Extensions• Requires CNDA staff

to generate.• CNDA creates

database tables, forms, etc.

• Best option for formal extensions.

<?xml version="1.0" encoding="UTF-8"?><xs:schema targetNamespace=http://nrg.wustl.edu/iq><xs:element name="IQAssessment" type="iq:iqData"/><xs:complexType name="iqData"><xs:complexContent><xs:extension base="subjectAssessorData"> <xs:sequence> <xs:element name="fsiq" minOccurs="0"> <xs:simpleType> <xs:restriction base="xs:integer">

<xs:minInclusive value="0"/><xs:maxInclusive value="200"/>

</xs:restriction> </xs:simpleType></xs:element><xs:element name="verbalIq" minOccurs="0">etc…

Non-imaging Data

Option 3: REDCap• Self-managed form- based

web application.• Details @

http://www.biostat.wustl.edu/redcap/

• Integration with XNAT underway

• Best option for managing your own non-imaging database.

CNDA Staff

Dan MarcusDirector

Jenny GurneyAssociate Director

John FlavinPipelines

Jeanette ClineHelpdesk

CNDA Training & Support• Training sessions

– 2nd Tuesday each month, 9:30 am, NRG Lab, #3334 East Building– Wednesday, July 16th, 2PM– Thursday, July 31st, 2PM

• Website– http://cnda-help.wustl.edu

• Helpdesk– [email protected]– (314) 286-0549– East Building Suite #3300

http://cnda-help.wustl.edu/

mailto:[email protected]

using the cnda

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