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3D Slicer Version 3.0 Update for mBIRN

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

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  1. 3D Slicer Version 3.0Update for mBIRN Analysis, Visualization, and Interpretation

  2. 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

  3. 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!

  4. 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)

  5. FreeSurfer • FreeSurfer Models and Volumes handled as built-in types • Scalar Overlays and Lookup Tables will be Supported

  6. 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

  7. 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

  8. QueryAtlas • Leverages FreeSurfer and Informatics Interoperability • Interactive Data Exploration for mBIRN and fBIRN • Ongoing Ontology Tie-in Work and Workflow Development

  9. 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

  10. 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

  11. 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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