Spring Meeting 2007

3D Slicer Version 3.0Update 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

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

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

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 Models and Volumes handled as built-in types

Scalar Overlays and Lookup Tables will be Supported

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

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

Leverages FreeSurfer and Informatics Interoperability

Interactive Data Exploration for mBIRN and fBIRN

Ongoing Ontology Tie-in Work and Workflow Development

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

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

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