Difference between revisions of "DBP2:MIND:Roadmap"

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=== Lesion segmentation ===
 
=== Lesion segmentation ===
 
A number of algorithms for fully or semi-automated lesion analysis will be evaluated. These include:
 
A number of algorithms for fully or semi-automated lesion analysis will be evaluated. These include:
:* EM-segment (Sandy Wells)
+
:* Slicer3 module EM-segment (Sandy Wells)
:* itkEMS Compare Lesion Analysis Tools (Prastawa/Gerhig)  
+
:* ITK stand-alone itkEMS Compare Lesion Analysis Tools (Prastawa/Gerhig)  
:* itk (Magnotta)
+
:* ITK stand-alone white matter lesion segmentation (Magnotta)
:* Manual tracing by clinically trained rater (Gasparovic/Bockholt)
+
:* Slicer3 Manual tracing by clinically trained rater (Gasparovic/Bockholt)
 
   
 
   
 
=== Lesion Localization ===
 
=== Lesion Localization ===
:* Slicer has tools for labeling white matter lesions and summarizing their anatomical location
+
:* Slicer3 has tools for labeling white matter lesions and summarizing their anatomical location
  
 
=== Lesion Load Measurement ===
 
=== Lesion Load Measurement ===
:* Slicer has tools for measurement of labelled lesions
+
:* Slicer3 has tools for measurement of labelled lesions
  
 
=== Performance characterization and validation ===
 
=== Performance characterization and validation ===

Revision as of 19:40, 17 March 2008

Home < 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 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

A number of algorithms 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/Gerhig)
  • ITK stand-alone white matter lesion segmentation (Magnotta)
  • 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

  • 5 Externally 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 (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)
    • we have tried EM-Segment
      • EM-Segment currently has a bug that does not permit 3 channel segmentation, it does work with 2 channel. Mantis ID#0000205
      • Em-Segment does not properly allow user to edit or change weighting of channels, this is crucial for hierarchical lesion classification. Mantis ID#0000204
    • UNC package so far
      • Marcel and Mark are in active collaboration with getting UNC method to work on-site, we have encountered compilation and memory problems with the package on mac and linux environments so far
    • as of 3/10/2008 we are working with Vince Magnotta on BRAINS2 method
  • Lesion Localization
  • 4/15/2008 complete lesion localizations and maps for EM-segment, BRAINS2, manual, UNC packages (Jeremy, Chuck, Vince Magnotta, Steve)
  • Lesion Measurement
  • 4/20/2008 complete lesion measurements and regional lesion load summaries for EM-segment, BRAINS2, manual, UNC packages (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
  • Consultant: Vincent Magnotta, University of Iowa
  • Host Institues: The MIND Institute and The University of New Mexico