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The Central Neuroimaging Data Archive Tools for storing, analyzing, and exploring neuroimaging data

The Central Neuroimaging Data Archive Tools for storing, analyzing, and exploring neuroimaging data. Dan Marcus Neuroinformatics Research Group December 19, 2007. What is the CNDA?. The CNDA: Central Neuroimaging Data Archive Precursor to the CNDA:

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The Central Neuroimaging Data Archive Tools for storing, analyzing, and exploring neuroimaging data

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  1. The Central Neuroimaging Data ArchiveTools for storing, analyzing, and exploring neuroimaging data Dan Marcus Neuroinformatics Research Group December 19, 2007

  2. What is the CNDA? • The CNDA: Central Neuroimaging Data Archive • Precursor to the CNDA: The Big Mess of Files Scattered across a Bunch of Computers, Tapes, and Binders Shoved in a File Cabinet Somewhere. • The mission of the CNDA: Organize & integrate neuroimaging and related data in order to improve its quality, usability, and long-term integrity.

  3. Neuroimaging Local users CNDA Processing & analysis Collaborators Community Related data What is the CNDA? Data storage Data integration Data processing Data access Data visualization Data exploration

  4. History of the CNDA 2002: Initiated to manage ADRC Neuroimaging 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 neuroimaging community

  5. The CNDA today • 2400 Subjects (458 ADRC) • 3400 MR Sessions (953 ADRC) • 2000 Whole brain tissue segmentations • 700 Radiological assessments • 400 Automated regional segmentations • 500 White matter disease assessments • 2000 Clinical assessments • 2000 Psychometric assessments • 200 CSF antibody assay • 500 PET Sessions • 0 Lost data sets

  6. Working with the CNDA • Navigating the website • The data stream • Storing and retrieving data • Processing data • Participating in the CNDA

  7. scanner The CNDA data stream ???

  8. scanner prearc The CNDA data stream

  9. scanner prearc The CNDA data stream

  10. scanner prearc The CNDA data stream http://nrg.wustl.edu/projects/DICOM

  11. scanner prearc The CNDA data stream

  12. scanner prearc The CNDA data stream /data/cninds01/data4/CNDA_CACHE/Prearc/ 20061213_095350/ 20061214_113454/ 20061214_123207/ head_Zacks_1.xml head_Zacks/ (many DICOM files)

  13. scanner prearc archive The CNDA data stream /data/cninds01/data1/CNDA_HOME/ arc001/ arc002/ arc_marcus1/ 060316_vc20616/ 060330_vc20770/ RAW/ (many DICOM files) PROCESSED/ (many 4dfp, Analyze, log, etc. files) ASSESSORS/ ASEG/ FSEG/ (more 4dfp, Analyze, data, etc. files) LOCAL/ (whatever you want) ----> /data/bluearc/marcus1 Owned and writable by ‘capweb’ Readable by investigator group Owned and writable by investigator group

  14. scanner prearc archive The CNDA data stream /data/cninds01/data1/CNDA_HOME/ arc001/ arc002/ arc_marcus1/ 060316_vc20616/ 060330_vc20770/ RAW/ (many DICOM files) PROCESSED/ (many 4dfp, Analyze, log, etc. files) ASSESSORS/ ASEG/ FSEG/ (more 4dfp, Analyze, data, etc. files) LOCAL/ (whatever you want) ----> /data/bluearc/marcus1 Subject data Assessments Derived measures Pointers to images CNDA database

  15. scanner prearc archive The CNDA data stream automated processing

  16. scanner prearc archive The CNDA data stream automated processing Existing processing pipelines T1, T2 atlas registration T1 morphometric analysis BOLD pre-processing Functional connectivity PET/MR registration PET time course analysis Freesurfer automated segmentation DTI (coming soon)

  17. scanner prearc archive The CNDA data stream automated processing http://nrg.wustl.edu

  18. scanner prearc archive The CNDA data stream automated processing <Pipeline> <name>StdBOLDPreprocessing</name> <steps> <step id="1" description="Prepare Folder Structure"> <step id="2" description="Prepare Bold Data" > <step id="3" description="Clean up"> <step id="4" description="Create List files"> <step id="5" description="Cross ReAlign"> <step id="6" description="Compute Mode 1000 Normalization"> <step id="7" description="Movement Analysis"> <step id="8" description="Make EPI first frame (anatomy) image"> <step id="9" description="Atlas Transformation"> <step id="10" description="Compute Atlas Transform "> <step id="11" description="Make Atlas Transformed EPI anat_ave in 333 and 222 atlas space" > <step id="12" description="Make Cross-realigned atlas-transformed resampled BOLD 4dfp stacks"> <step id="13" description="Run var_4dfp -sn4 on both *xr3d_norm and *xr3d_atl and make movies"> <step id="14" description="Launch Functional Connectivity PreProcessing Script">

  19. scanner prearc archive The CNDA data stream automated processing <step id="6" description="Compute Mode 1000 Normalization"> <resource name="normalize_4dfp" location="/data/cninds01/data2/pipeline-tools/catalog/nilResources"> <argument id="4dfp_file"> <value>concat('sessionId','_b',PIPELINE_LOOPON(irun),'_faln_dbnd_r3d_avg')</value> </argument> </resource> <output id="normalize_4dfp:4dfp File"> <file xsiType="xnat:imageResource"> <content>R3D_AVG_NORM</content> </file> </output> </step>

  20. scanner prearc archive user The CNDA data stream

  21. scanner prearc archive user The CNDA data stream http://nrg.wustl.edu/projects/fiv

  22. scanner prearc archive user The CNDA data stream

  23. scanner prearc archive archive archive archive user automated processing automated processing automated processing The CNDA data stream

  24. Network issues WUSTL/WUCON neuroimage Conte storage VPN CNDA NIL users Conte users

  25. Network issues Shared neuroimage/WUCON CNDA NIL users Conte users Conte storage

  26. scanner prearc archive user The CNDA data stream automated processing

  27. scanner prearc archive user The CNDA data stream automated processing • Quality control features • Prearchive • Automation • Provenance • Online image viewing • Study-specific validation • Annotation

  28. An invitation to participate in the CNDA • Register: http://cnda.neuroimage.wustl.edu • Contact me: dmarcus@wustl.edu • Start sending your data • Levels of participation • Convenient storage and access • Utilize standard processing pipelines • Integrate non-imaging data • Custom pipelines & tools

  29. Neuroinformatics Research Group (NRG) Mohana Ramaratnam, Dan Marcus, Tim Olsen, Kevin Archie Our collaborators & partners: NIL: Marc Raichle, Avi Snyder, Mark Mintun, Mike Fox CSG: Ben Pflanz, Steve Wiese Psychology: Denise Head, Bill Janes, Erin Laciny, Lindsay Casmaer ADRC: John Morris, Phil Miller, Betsy Grant, Kathy Roe Harvard: Randy Buckner, Glenn Hoffman BIRN

  30. The CNDA website

  31. The CNDA website

  32. The CNDA website

  33. The CNDA website

  34. The CNDA website

  35. The CNDA website

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