using the cnda
DESCRIPTION
Using the CNDA. Dan Marcus & CNDA Staff July 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. - PowerPoint PPT PresentationTRANSCRIPT
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Using the CNDA
Dan Marcus & CNDA StaffJuly 11, 2014
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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
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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.
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The CNDA Today
• > 400 active users• > 1,100 registered projects• > 32,000 subjects• > 49,000 sessions• > 50 TB total storage
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Demo!
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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).
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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.
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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.
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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
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(0008,1030) Study Description OR(0008,0050) Accession Number (0010,0010) Patient's
Name
(0010,0020) Patient ID
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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.
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Option 1: Web uploader
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Option 1: Web uploader
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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.
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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.
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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.
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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
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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.
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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
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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)
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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
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Accessing Data: Web download
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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
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Accessing Data: File System
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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
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Accessing Data: XNAT Gateway
Modality Workstation
CNDA
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Accessing Data: XNAT Gateway
Modality Workstation
CNDA
DICOM?DICOM
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Accessing Data: XNAT Gateway
Modality Workstation
CNDA
DICOM?DICOMHTTPS
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Accessing Data: XNAT Gateway
Modality Workstation
CNDA
DICOM?DICOMHTTPS
XNAT Gateway: DICOM adapter
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Accessing Data: XNAT Gateway
https://wiki.xnat.org/display/XNAT/XNAT+Gateway+Server+User+Manual
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Accessing Data: XNAT Gateway
https://wiki.xnat.org/display/XNAT16/XNAT+Gateway+Setup+for+Osirix
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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.
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Image Processing Pipelines
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Non-imaging Data
Option 1: Custom Variables• Do it yourself from
project page.• Appear on data edit
screens.• Best option for
small extensions.
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Non-imaging Data
Option 1: Custom Variables• Do it yourself from
project page.• Appear on data edit
screens.• Best option for
small extensions.
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Non-imaging Data
Option 1: Custom Variables• Do it yourself from
project page.• Appear on data edit
screens.• Best option for
small extensions.
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Non-imaging Data
Option 1: Custom Variables• Do it yourself from
project page.• Appear on data edit
screens.• Best option for
small extensions.
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Non-imaging Data
Option 2: Schema Extensions• Requires CNDA staff
to generate.• CNDA creates
database tables, forms, etc.
• Best option for formal extensions.
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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…
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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.
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CNDA Staff
Dan MarcusDirector
Jenny GurneyAssociate Director
John FlavinPipelines
Jeanette ClineHelpdesk
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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
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Q&A!