na-mic national alliance for medical image computing robust cerebrum and cerebellum segmentation...
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
National Alliance for Medical Image Computing http://na-mic.org
Robust Cerebrum and Cerebellum Segmentation for Neuroimage Analysis
Jerry L. Prince, Aaron Carass, Lotta Ellingsen,
and Min Chen
Johns Hopkins University
Ron Kikinis and Nicole Aucoin
Brigham and Women’s Hospital
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National Institute on Biomedical Imaging and Bioengineering 1 R21 EB009900-01
National Alliance for Medical Image Computing http://na-mic.org
“Skull Stripping”
• Isolate the brain in MR images
• Existing algorithms yield inconsistent results
human rater is still gold standard
• SPECTRE is a “hybrid” technique (top-down and bottom-up) that preserves cortical gray matter and yields high Dice coefficients
Typical SPECTRE result
SPECTRE Result on patient
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National Alliance for Medical Image Computing http://na-mic.org
Features
• Do not be overly aggressive:– affects quantification (thickness)
of cortical gray matter– affects determination of pial
layer
• Provide added flexibility:– separate hemispheres,
cerebrum, cerebellum and brain stem
• Rigorously validate:– evaluate on thousands of highly
varied data sets– compare with existing
algorithms
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Manual Result
Some cortex is “stripped” away
National Alliance for Medical Image Computing http://na-mic.org
Project Overview
Goal: Develop and augment the SPECTRE algorithm as a module within the NA-MIC Kit software environment—e.g., 3DSlicer. (Funded NIBIB R21)
SPECTRE = Simple Paradigm for Extra Cerebral Tissue REmoval
Specific aims:
1. Rewrite SPECTRE using the Free Open Source Software Development Methodology of NA-MIC. [Hopkins, BWH, Mostly Year 1]*
2. Complete the algorithms necessary for isolating and establishing a coordinate system on the cerebellum. [Hopkins, Years 1 and 2]
3. Parameters will be optimized in order for SPECTRE to perform well with a variety of differently acquired data. [Hopkins, Years 1 and 2]
4. Compare SPECTRE against all available publicly available (source or binary) skullstripping software. [Hopkins, BWH, Mostly Year 2]
*Or: Make SPECTRE a module within 3DSlicer
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National Alliance for Medical Image Computing http://na-mic.org
SPECTRE Basics
• A watershed principle is at the core of SPECTRE– Works according to intensity
ordering of WM, GM, CSF in MR images
• Initial masks are found by multiple atlas registration– cerebrum, cerebellum, brain
stem, and whole brain
• classification, morphology, topology, and watershed algorithms are then applied– sanity checks are applied
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National Alliance for Medical Image Computing http://na-mic.org
History and Status
• SPECTRE was originally implemented in C/C++– ISBI conference paper in 2007
• SPECTRE was ported to JAVA in order to operate within the Java Image Science Toolkit (JIST environment)– JIST is an open source pipeline and medical image processing
environment: http://www.nitrc.org/projects/jist/
• Further development and testing has been carried out on the Java code within JIST – a journal paper is in the final preparation stage
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National Alliance for Medical Image Computing http://na-mic.org
Algorithm Progress
• Cerebellum isolation • Hemisphere separation
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National Alliance for Medical Image Computing http://na-mic.org
Performance Evaluation
• Data sets and results– 25 older subjects, cerebrum,
two raters– 3 subjects, repeat scans– 1046 scans, older subjects,
cerebrum, one rater
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Worst result
National Alliance for Medical Image Computing http://na-mic.org
What is JIST?
• It is a visual interface, pipeline tool, and collection of 3D image analysis modules
• It works in concert with MIPAV
• Modules can run from a command line interface
• Java platform independent
• Designed for large-scale runs
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National Alliance for Medical Image Computing http://na-mic.org
Early Integration Status• Java SPECTRE requires Java
Runtime environment (JRE) and JIST and MIPAV
3DSlicer is being extended to load JRE [BWH]
SPECTRE and libraries are being rolled up in a comprehensive JAR file [JHU]
• The SPECTRE module is described by an XML file that is scanned by 3DSlicer and incorporated as a command line module
XML descriptor is being written [JHU]
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National Alliance for Medical Image Computing http://na-mic.org
SPECTRE 2009• Creation of SPECTRE 2009
graphical interface in 3DSlicer is automatic– Required JIST CLI mods
– Done this week, shown in right
• Limitations– no shared memory between
SPECTRE and 3DSlicer
– memory requirements overall are large: 1-1.5GB for SPECTRE
• Benefits– Mechanism permits other modules
to become available to 3DSlicer
– Future SPECTRE development works in JIST, MIPAV, and NA-MIC
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National Alliance for Medical Image Computing http://na-mic.org
Future Work
• Release initial version as 3DSlicer plugin– Complete CLI support for JIST/Java in 3DSlicer– Fix Windows Java problem
• Incorporate MGDM for joint cerebrum, cerebellum, and brainstem isolation – Validate MGDM in Java– Augment OASIS atlases with additional labels
• Carry out extensive validations– cerebellum, 20 subject repeat scans, tumor cases
• Optimize SPECTRE speed, flexibility, visualization interactivity
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