DBP2:MIND:Roadmap

Back to NA-MIC Internal Collaborations, MIND DBP 2

Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus

Objective

We would like to create an end-to-end application entirely within NA-MIC Kit allowing individual analysis of white matter lesions. Such a workflow applied to lupus patients is one of 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 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 detected 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

We will obtain gray matter, white matter, CSF, and lesion maps for each subject based on T1-weighted, T2-weighted, and FLAIR images. 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.

The current status of the main modules to be used are:

Registration

• ITK has mutual information registration
  • T1/T2/Flair co-registration implemented into EM-segment module

Lesion segmentation

Three algorithms (all within NA-MIC kit) for fully or semi-automated lesion analysis will be evaluated. These include:

• Slicer3 module EM-segment (Sandy Wells)
• ITK stand-alone itkEMS Compare Lesion Analysis Tools (Prastawa/Gerig)
• ITK stand-alone white matter lesion segmentation (Magnotta)

Manual tracing will serve as a bronze-standard:

• Slicer3 Manual tracing by clinically trained rater (Gasparovic/Bockholt)

Lesion Localization

• Slicer3 has tools for labeling white matter lesions and summarizing their anatomical location

Lesion Load Measurement

• Slicer3 has tools for measurement of labelled lesions

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 the 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

• 10 Externally sharable T1,T2,Flair,Lesion Map data-sets (NIFTI format) will be made available
  • 5 from subjects with lupus and 5 healthy normal volunteers
• A tutorial will be created that will guide end-users through each step needed to complete a lesion analysis in the NA-MIC kit
  • A step-by-step guide will be produced for one example lupus cases within the tutorial and one example healthy normal volunteer
  • Measurements for all 10 subjects will also be provided

Schedule

• Sequence Optimization and Data Collection

• 10/15/2007 T1, T2, FLAIR optimized sequences for Siemens 3T Trio Tim scanner (Jeremy, Bruce, Chuck)
  • We will work with Bruce Fischl on using MEMPR, Mugler, and FLAIR sequences that have been optimized for maximum constrast and minimal geometric distortion across sequences
  • DONE
• 3/31/2008 collection of 5 lupus subjects on clinical sequence and optimized 3T sequence (Chuck)
  • collected 2 patients and 3 controls so far
    • as of 3/10/2008 there are 3-4 additional patients scheduled, since january 1, we have had 4 patients not able to complete the protocol so far

• Co-Registration and Atlas Registration

• 1/31/2008 optimized mutual information registration for clinical sequences and optimized 3T sequences (Jeremy)
  • we have tried the registration tools built-in to Slicer 3 EM-segment module so far
  • DONE Brad has implemented this successfully into the EM-segment module

• Lesion segmentation

• 3/31/2008 complete lesion segmentation methods for EM-segment, BRAINS2, manual, UNC packages (Jeremy, Chuck, Vince Magnotta, Kilian/Brad, Marcel)
  • Slicer3 EM-segment Module
    • Currently has a bug that does not permit 3 channel segmentation Mantis ID#0000205
      • Only using 2 channels such as T1/T2 or T1/Flair does not produce sensible/usable results
    • Does not properly allow user to edit or change weighting of channels, this is crucial for hierarchical lesion classification. Mantis ID#0000204
  • ITK itkEMS stand-alone package
    • Marcel and Mark are in active collaboration with getting this method to work on-site, we have encountered compilation and memory problems with the package on mac and linux environments so far
  • ITK lesion classification stand-along package
    • Vince Magnotta has develop an ITK-based 2 stage lesion segmentation method
      • stage one uses k-means tissue classification into grey, white, or csf of co-registered T1/T2
      • stage two use bayesian classifier into normal tissue or lesion using results of stage one and co-reigstered Flair
  • Slicer3 Manual Tracing
    • Gasparovic has manually traced all tutorial cases with lesions using T2/Flair images following tracing guidelines and a qualitative neuroradiological review report
      • 4/1/2008 create manual tracing guidelines documentation and share here

• Lesion Localization

• 4/15/2008 complete lesion localizations and maps for Slicer3 EM-segment, ITK itkEMS, ITK lesion segmentation, and Slicer3 manual tracing (Jeremy, Chuck, Vince Magnotta, Steve)

• Lesion Measurement

• 4/20/2008 complete lesion measurements and regional lesion load summaries for Slicer3 EM-segment, ITK itkEMS, ITK lesion segmentation, and Slicer3 manual tracing (Jeremy, Chuck, Vince Magnotta, Steve)

• Performance characterization and validation

• 1/6/2008 report to 2008 NA-MIC AHM on progress for performance and validation of lesion segmentation methods for EM-segment, BRAINS2, manual, UNC packages (Jeremy)
  • DONE
• 5/15/2008 submit abstract on reliability and summary of novel NA-MIC kit lesion analysis method (Jeremy, Chuck, Mark Scully, Brad, Kilian, others)
  • plan is to submit SFN abstract and manuscript closely after
• 5/20/2008 analyze NIH study clinical sample using NA-MIC kit lesion analysis method (Jeremy, Chuck, Mark Scully)
• 7/1/2008 submit manuscript on clinical application of NA-MIC kit lesion analysis method (Jeremy, Chuck, Mark Scully, Carlos Roldan, Bill Sibbitt)

• Incorporation of approach into NA-MIC kit

• 1/6/2008 Slicer3 Lesion Analysis Module that handles co-registration of T1, T2, and Flair (Mark Scully, Steve)
  • DONE Brad completed this
• 5/1/2008 extend Slicer3 Lesion Analysis Module to handle lesion localization and measurement ('Mark Scully, Steve)
  • in progress
• 6/1/2008 extend Slicer3 Lesion Analysis Module to implement the lesion analysis method (EM-segment, BRAINS2, UNC packages) with the best performance (Mark Scully, Steve)
  • a demonstration will be given at the 2008 NA-MIC AHM--we would consider this version a prototype and would be testing, refining the module through the clinical application phase (Jeremy, Mark Scully)
• 6/20/2008 functioning version of lesion analysis Slicer3 Module complete (Mark Scully, Steve)

• Tutorial and Data-sharing

• 7/1/2008 make data sets and tutorial available to the public (Mark Scully, Jeremy, Sonja)
  • If we submit SFN abstract, we can advertise the availability during SFN Conference in November 2008
    • We could think about advertising the roadmaps at the BIRN booth at SFN this year?
• 6/20/2008 present tutorial to 2008 NA-MIC programming week (Mark Scully, Jeremy, Sonja)

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: Ross Whitaker, Utah
• Kilian Pohl
• Brad Davis
• Marcel Prastawa
• Consultant: Vincent Magnotta, University of Iowa
• Host Institues: The MIND Institute and The University of New Mexico