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Using the CNDA

Learn about CNDA: its history, features, security, data upload methods, and data storage costs. Access data via web download or file system. Get insights on imaging metadata and collaboration.

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Using the CNDA

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  1. Using the CNDA Dan Marcus & CNDA Staff July 11, 2014

  2. 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

  3. 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.

  4. The CNDA Today • > 400 active users • > 1,100 registered projects • > 32,000 subjects • > 49,000 sessions • > 50 TB total storage

  5. Demo!

  6. 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).

  7. 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.

  8. 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.

  9. Image Upload: DICOM mappings

  10. (0010,0020) Patient ID (0008,1030) Study Description OR (0008,0050) Accession Number (0010,0010) Patient's Name

  11. 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.

  12. Option 1: Web uploader

  13. Option 1: Web uploader

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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)

  21. 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

  22. Accessing Data: Web download

  23. 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: • sshfsdmarcu01@login1.nrg.wustl.edu:/data/CNDA/archive/CONDR_METS . -o defer_permissions -o volname=CONDR_METS

  24. Accessing Data: File System

  25. 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

  26. Accessing Data: XNAT Gateway CNDA Workstation Modality

  27. Accessing Data: XNAT Gateway CNDA Workstation DICOM? DICOM Modality

  28. Accessing Data: XNAT Gateway CNDA Workstation DICOM? DICOM Modality HTTPS

  29. Accessing Data: XNAT Gateway CNDA Workstation DICOM? DICOM Modality HTTPS XNAT Gateway: DICOM adapter

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

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

  32. 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.

  33. Image Processing Pipelines

  34. Non-imaging Data Option 1: Custom Variables • Do it yourself from project page. • Appear on data edit screens. • Best option for small extensions.

  35. Non-imaging Data Option 1: Custom Variables • Do it yourself from project page. • Appear on data edit screens. • Best option for small extensions.

  36. Non-imaging Data Option 1: Custom Variables • Do it yourself from project page. • Appear on data edit screens. • Best option for small extensions.

  37. Non-imaging Data Option 1: Custom Variables • Do it yourself from project page. • Appear on data edit screens. • Best option for small extensions.

  38. Non-imaging Data Option 2: Schema Extensions • Requires CNDA staff to generate. • CNDA creates database tables, forms, etc. • Best option for formal extensions.

  39. Non-imaging Data <?xml version="1.0" encoding="UTF-8"?> <xs:schematargetNamespace=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… Option 2: Schema Extensions • Requires CNDA staff to generate. • CNDA creates database tables, forms, etc. • Best option for formal extensions.

  40. 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.

  41. CNDA Staff Dan Marcus Director Jenny Gurney Associate Director John Flavin Pipelines Jeanette Cline Helpdesk

  42. 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

  43. Q&A!

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