DBP2:MIND:Roadmap

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.

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

• 10/15/2007 T1, T2, FLAIR optimized sequences for Siemens 3T Trio Tim scanner

• Registration

• 10/1/2007 - White matter/gray matter segmentation of the young brain using itkEMS as a Slicer3 module (C Vachet) - at AHM

• Lesion segmentation

• Lesion Localization

• Performance characterization and validation

• Tutorial