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3D Slicer Version 3.0 Update for mBIRN. Analysis, Visualization, and Interpretation. What is Slicer3?. Total Rework of 3D Slicer At least 80% of code rewritten New versions of VTK (5.0), ITK (3.2) Improved Look and Feel (KWWidgets) Improved Modularity

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3d slicer version 3 0 update for mbirn

3D Slicer Version 3.0Update for mBIRN

Analysis, Visualization, and Interpretation

what is slicer3
What is Slicer3?
  • Total Rework of 3D Slicer
    • At least 80% of code rewritten
    • New versions of VTK (5.0), ITK (3.2)
    • Improved Look and Feel (KWWidgets)
    • Improved Modularity
      • Analysis routines can be used as plugins or command line executables for batch processing
    • Draws on Multi-Institution Community
      • Kitware, Inc., GE Research, Isomics, Inc., BWH, UCLA, UCSD, UIowa, MIT, GaTech, UNC, U Utah, MGH, UCI, Harvard, WashU…
      • NAC, NCIGT, NA-MIC, mBIRN, fBIRN
slicer3 usability
Slicer3 Usability
  • Clean, Unified GUI Design
    • Wendy Plesniak (BWH) and Sebastien Barre (Kitware)
  • Developed in Close Collaboration with User Community and Trainers
  • Unified Cross Platform Behavior, Easy Installers
  • Undo/Redo, Tooltips, Drag ‘n’ Drop…
  • New Logo!
mbirn slicer goals
mBIRN Slicer Goals
  • Ensure mBIRN Slicer functionality stays current with new Slicer version
    • FreeSurfer Interoperability
    • DTI Analysis and Visualization
    • Provenance
    • QueryAtlas
    • BIRNDUP
    • Protocol Neutral Segmentation (EM Segmenter)
    • Informatics Interoperability (XNAT, Portal, Grid, Workflows)
freesurfer
FreeSurfer
  • FreeSurfer Models and Volumes handled as built-in types
  • Scalar Overlays and Lookup Tables will be Supported
dti analysis and visualization
DTI Analysis and Visualization
  • Under Active Development but not yet ready
    • Expected by late 2007
  • Developed with NA-MIC, NAC, LMI, and NCIGT
  • Applications in Image Guided Neurosurgery will Help Drive Development
provenance
Provenance
  • Built in from beginning of Slicer3
  • Track Cross-Platform Issues
    • Windows (XP and soon Vista)
    • Mac OSX (PPC and X86)
    • Linux (32 and 64 bit)
  • Being Integrated with Slicer3 Execution Model
    • Parameters developed with interactive Slicer environment
    • Modules can run as independent batch jobs on cluster or grid using those parameters
queryatlas
QueryAtlas
  • Leverages FreeSurfer and Informatics Interoperability
  • Interactive Data Exploration for mBIRN and fBIRN
  • Ongoing Ontology Tie-in Work and Workflow Development
birndup
BIRNDUP
  • Can be ported to Slicer3
    • Delayed pending development of mBIRN policy for defacing
  • Command line tools for DICOM Header Deidentification publicly available and documented
protocol neurtral segementation
Protocol Neurtral Segementation
  • EM Segmenter being ported to Slicer3 by MIT and Kitware
    • Tutorial held January 2007 in Utah
    • Documentation on the Web
  • Additional development ongoing
  • Slicer2 version successfully used in MS Lesion segmentation
  • Included in the current 3D Slicer 2.6
  • Applied to white matter lesion segmentation in Multiple Sclerosis.
  • MPRAGE and FLAIR
  • Available to support BELL
  • Data courtesy Istvan Csapo, Charles Guttmann, Center for Neurological Imaging, Brigham and Women’s Hospital. Algorithm by Kilian Pohl, MIT/BWH/Isomics
xnat informatics integration
XNAT / Informatics Integration
  • Current Status:
    • Query/Browse for Data at XNAT Site (oasis-brains.org)
    • Download XAR (zip) from XNAT
    • Tell Browser to “Open With…” Slicer3
    • Images Available for Visualization and Analysis
  • Next Steps
    • Manifest / Data Description files / XCEDE
    • FreeSurfer Datasets, DTI Datasets in XNAT
    • Upload of Processed Data
    • Direct Database Interface (Improve download performance)
    • Generalize for BDR
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