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Using the CNDA

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.

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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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