1 / 11

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

mckenzie-harmon
Download Presentation

3D Slicer Version 3.0 Update for mBIRN

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related