Transcript CNDA overview
Using the CNDA Dan Marcus & CNDA Staff July 11, 2014
What is the CNDA?
QUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESS IMAGING METADATA OTHER SOURCES
• Data archiving • Quality control • Data access • Security • 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 • • • • • > 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
(0008,1030) Study Description OR (0008,0050) Accession Number (0010,0010) Patient's Name (0010,0020) Patient ID (0020,0011) Series Number (0008,103E) Series Description (0010,4000) OR Patient Comments (0032,4000) Study Comments
CNDA Field
Project Subject Label Session Label Scan Number Series Description 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
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 • • • • • • • 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/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 Workstation Modality
Accessing Data: XNAT Gateway Modality DICOM CNDA DICOM?
Workstation
Accessing Data: XNAT Gateway Modality DICOM CNDA DICOM?
HTTPS Workstation
Accessing Data: XNAT Gateway Modality DICOM CNDA DICOM?
HTTPS Workstation 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://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 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.
Non-imaging Data • • • • Option 3: REDCap Self-managed form based 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 – 2 nd Tuesday each month, 9:30 am, NRG Lab, #3334 East Building – Wednesday, July 16 th , 2PM – Thursday, July 31 st , 2PM Website – http://cnda-help.wustl.edu
Helpdesk – [email protected]
– (314) 286-0549 – East Building Suite #3300
Q&A!