Using the CNDA
Dan Marcus & CNDA Staff
July 11, 2014
What is the CNDA?
QUARANTINE
LOCAL USE
COLLABORATION
PUBLIC ACCESS
IMAGING
METADATA
OTHER SOURCES
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Data archiving
Quality control
Data access
Security
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Visualization
Automation
Integration
Data sharing
History of the CNDA
2002: 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
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> 400 active users
> 1,100 registered projects
> 32,000 subjects
> 49,000 sessions
> 50 TB total storage
Demo!
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 mappings
DICOM Field
CNDA Field
(0008,1030)
OR
(0008,0050)
Study Description
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)
OR
(0032,4000)
Patient Comments
Comma-separated list of project,
subject, session
Accession Number
Study Comments
(0008,1030) Study
Description OR
(0008,0050) Accession
Number
(0010,0020) Patient ID
(0010,0010) Patient's
Name
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
Image Upload: Remote Sites
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.
Image Upload: Remote Sites
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 Scans
Option 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 Scans
Option 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 Scans
Option 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
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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
helpdesk@nrg.wustl.edu).
• Request read access to your project directory.
• Access on nrg cluster:
– ssh dmarcu01@login1.nrg.wustl.edu
– cd /data/CNDA/archive/CONDR_METS
• Mount on local computer:
– sshfs
dmarcu01@login1.nrg.wustl.edu:/data/CNDA/archive/CO
NDR_METS . -o defer_permissions -o
volname=CONDR_METS
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
CNDA
Modality
Workstation
Accessing Data: XNAT Gateway
CNDA
Workstation
Modality
DICOM
DICOM?
Accessing Data: XNAT Gateway
CNDA
Workstation
Modality
DICOM
DICOM?
HTTPS
Accessing Data: XNAT Gateway
CNDA
Workstation
Modality
DICOM
DICOM?
HTTPS
XNAT Gateway:
DICOM adapter
Accessing Data: XNAT Gateway
https://wiki.xnat.org/display/XNAT/XNAT+Gateway+Server+User+Manual
Accessing Data: XNAT Gateway
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://cndahelp.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 1: Custom
Variables
• Do it yourself from
project page.
• Appear on data edit
screens.
• Best option for
small extensions.
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 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 formbased web application.
• Details @
http://www.biostat.wus
tl.edu/redcap/
• Integration with XNAT
underway
• Best option for
managing your own
non-imaging database.
CNDA Staff
Dan Marcus
Director
Jenny Gurney
Associate Director
John Flavin
Pipelines
Jeanette Cline
Helpdesk
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
– cnda-help@wustl.edu
– (314) 286-0549
– East Building Suite #3300
Q&A!