1. 3D Slicer Version 3.0 Update 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