Difference between revisions of "DBP2:MIND:Roadmap"
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==Objective== | ==Objective== | ||
| − | We would like to create an end-to-end application within NA-MIC Kit allowing individual | + | 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 | * '''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. | * '''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 Localization''': Each unique lesion should be detacted and anatomical location summarized | ||
* '''Lesion Load Measurement''': Measure volume of each lesion, summarize lesion load by regions | * '''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 |
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=== Performance characterization and validation === | === 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. | |
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Revision as of 09:52, 27 September 2007
Home < DBP2:MIND:RoadmapContents
Brain 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 labelling
- BRAINS2
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.
