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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