Difference between revisions of "DBP2:MIND:Roadmap"
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* Performance characterization and validation | * Performance characterization and validation | ||
:* '''1/10/2007''' report to NA-MIC AHM on performance and validation of lesion segmentation methods for EM-segment, BRAINS2, manual, MedX, UNC packages | :* '''1/10/2007''' report to NA-MIC AHM on performance and validation of lesion segmentation methods for EM-segment, BRAINS2, manual, MedX, UNC packages | ||
− | :* '''2/15/2007''' '''submit manuscript on reliability and summary of NA-MIC kit lesion analysis method''' | + | :* '''2/15/2007''' '''submit manuscript on reliability and summary of novel NA-MIC kit lesion analysis method''' |
− | :* '''3/15/2007''' '''submit manuscript on clinical application of NA-MIC kit lesion analysis method''' | + | :* '''3/15/2007''' analyze NIH study clinical sample using NA-MIC kit lesion analysis method |
+ | :* '''4/15/2007''' '''submit manuscript on clinical application of NA-MIC kit lesion analysis method''' | ||
* Tutorial and Data-sharing | * Tutorial and Data-sharing | ||
− | :* ''' | + | :* '''5/1/2007''' '''make data sets and tutorial publically available''' |
Revision as of 10:27, 27 September 2007
Home < DBP2:MIND:RoadmapBrain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus
Objective
We would like to create an end-to-end application within NA-MIC Kit allowing individual analysis of white matter lesions. Such a workflow applied to lupus patients is one goals of the MIND DBP. This page describes the technology roadmap for lesion analysis in the NA-MIC Kit. The basic components necessary for this end-to-end application are:
- Registration: co-registration of T1-weighted, T2-weighted, and FLAIR images
- Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work on non-skull-stripped data.
- Lesion Localization: Each unique lesion should be detacted and anatomical location summarized
- Lesion Load Measurement: Measure volume of each lesion, summarize lesion load by regions
- Tutorial: Documentation will be written for a tutorial and sample data sets will be provided
Roadmap
Starting with several MRI images (weighted-T1, weighted-T2, FLAIR...) we want to obtain lesion maps for each subject. Ultimately, the NA-MIC Kit will provide a workflow for individual and group analysis of lesions. It will be implemented as a set of Slicer3 modules that can be used interactively within the Slicer3 application as well as in batch on a computing cluster using BatchMake.
Next we discuss the main modules and details of current status and development work:
Registration
- ITK has mutual information registration
- BRAINS2 has AIR package wrapped
Lesion segmentation
A number of algorithms for fully or semi-automated lesion analysis will be evaluated on brain images from subjects in a study on lupus erythematosis. These include:
- UNC has a tool called itkEMS Compare Lesion Analysis Tools (marcel)
- EM-segment (sandy wells)
- MedX (commercial package)
- BRAINS2 (magnotta)
- manual tracing by clinically trained rater
Lesion Localization
- Freesurfer has tools for labeling white matter lesions and summarizing their anatomical location
- BRAINS2 has tools for creating masks for white matter lesions and summarizing their anatomical location
Lesion Load Measurement
- Freesurfer has tools for measurement of labelled lesions
- BRAINS2 has tools for measurement of lesions and regional summaries
Performance characterization and validation
- Data will be collected at both 1.5 and 3T. Data at 1.5T will be obtained with the protocol utilized for current project on lupus at UNM.
- Data at 3T will be obtained with sequences optimized for segmentation by the group at Utah.
- Comparisons will be based on the approach developed by Martin-Fernandez et al.
- The algorithm with the best performance will be incorporated into the NA-MIC kit.
Tutorial
- 5 Publically sharable T1,T2,Flair,Lesion Map data-sets (NIFTI format) will be made available
- A tutorial will be created that will guide end-users through each step needed to complete a lesion analysis in the NA-MIC kit
Schedule
- Sequence Optimization and Data Collection
- 10/15/2007 T1, T2, FLAIR optimized sequences for Siemens 3T Trio Tim scanner
- 11/15/2007 collection of 5 lupus subjects on clinical sequence and optimized 3T sequence
- Registration
- 10/30/2007 optimized mutual information registration for clinical sequences and optimized 3T sequences
- Lesion segmentation
- 11/30/2007 complete lesion segmentation methods for EM-segment, BRAINS2, manual, MedX, UNC packages
- Lesion Localization
- 11/30/2007 complete lesion localizations and maps for EM-segment, BRAINS2, manual, MedX, UNC packages
- Performance characterization and validation
- 1/10/2007 report to NA-MIC AHM on performance and validation of lesion segmentation methods for EM-segment, BRAINS2, manual, MedX, UNC packages
- 2/15/2007 submit manuscript on reliability and summary of novel NA-MIC kit lesion analysis method
- 3/15/2007 analyze NIH study clinical sample using NA-MIC kit lesion analysis method
- 4/15/2007 submit manuscript on clinical application of NA-MIC kit lesion analysis method
- Tutorial and Data-sharing
- 5/1/2007 make data sets and tutorial publically available
Team and Institute
- Co-PI: H Jeremy Bockholt (jbockholt at mrn.org)
- Co-PI: Charles Gasparovic (chuck at unm.edu)
- Software Engineer: Mark Scully (mscully at mrn .org)
- NA-MIC Engineering Contact: Steve Pieper, Isomics
- NA-MIC Algorithms Contact: Bruce Fischl, MGH
- Host Institues: The MIND Institute and The University of New Mexico