The Central Neuroimaging Data Ar

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The Central Neuroimaging Data Ar Powered By Docstoc
					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:
    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.
                  What is the CNDA?

                                           Local users
Neuroimaging


                       CNDA
 Processing                                Collaborators
 & analysis

  Clinical
                      Data storage
  Diagnosis ___
  BP ___ / ___
  Meds ______         Data integration
Related data          Data processing      Community

                      Data access
                      Data visualization
                      Data exploration
        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
              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
        Working with the CNDA
•   Navigating the website
•   The data stream
•   Storing and retrieving data
•   Processing data
•   Participating in the CNDA
          The CNDA data stream
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          ???
          The CNDA data stream
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          The CNDA data stream
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          The CNDA data stream
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                       http://nrg.wustl.edu/projects/DICOM
          The CNDA data stream
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            The CNDA data stream
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/data/cninds01/data4/CNDA_CACHE/Prearc/
          20061213_095350/
          20061214_113454/
          20061214_123207/
               head_Zacks_1.xml
               head_Zacks/
                     (many DICOM files)
              The CNDA data stream
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/data/cninds01/data1/CNDA_HOME/
 arc001/
 arc002/
 arc_marcus1/ ----> /data/bluearc/marcus1
  060316_vc20616/
  060330_vc20770/
         RAW/                                             Owned and writable by
           (many DICOM files)                             ‘capweb’
         PROCESSED/                                       Readable by investigator
           (many 4dfp, Analyze, log, etc. files)          group
         ASSESSORS/
           ASEG/
           FSEG/
             (more 4dfp, Analyze, data, etc. files)
           LOCAL/                                          Owned and writable by
             (whatever you want)                           investigator group
              The CNDA data stream
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/data/cninds01/data1/CNDA_HOME/
 arc001/
 arc002/
 arc_marcus1/ ----> /data/bluearc/marcus1
  060316_vc20616/
  060330_vc20770/
         RAW/
           (many DICOM files)                                    Subject data
         PROCESSED/                                              Assessments
           (many 4dfp, Analyze, log, etc. files)                 Derived measures
         ASSESSORS/                                              Pointers to images
           ASEG/
           FSEG/
             (more 4dfp, Analyze, data, etc. files)
           LOCAL/
             (whatever you want)                                CNDA database
          The CNDA data stream
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                             automated
                             processing
            The CNDA data stream
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                                          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)
          The CNDA data stream
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                             automated
                             processing




                       http://nrg.wustl.edu
                 The CNDA data stream
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                                                                     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">
               The CNDA data stream
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                                                                    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>
          The CNDA data stream
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          The CNDA data stream
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                            http://nrg.wustl.edu/projects/fiv
          The CNDA data stream
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              The CNDA data stream
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          archive                 archive                archive




                automated               automated              automated
                processing              processing             processing
            Network issues
    neuroimage          WUSTL/WUCON




                  VPN                 Conte
                                      storage



         CNDA
 NIL                     Conte
users                    users
          Network issues
        Shared neuroimage/WUCON




            CNDA
 NIL                              Conte
users                             users

                        Conte
                        storage
          The CNDA data stream

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                            automated
                            processing
          The CNDA data stream

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                                     automated
                                     processing
 Quality control features
    Prearchive
    Automation
    Provenance
    Online image viewing
    Study-specific validation
    Annotation
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
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
The CNDA website
The CNDA website
The CNDA website
The CNDA website
The CNDA website
The CNDA website

				
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