Difference between revisions of "DBP2:MIND:Roadmap"

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* Lesion segmentation
 
* Lesion segmentation
:* '''3/31/2008''' complete lesion segmentation methods for Slicer3 EM-segment, ITK itkEMS, ITK lesion segmentation, and Slicer3 manual tracing ('''Jeremy, Chuck, Vince Magnotta, Kilian/Brad, Marcel''')
+
:* '''3/17/2008''' complete lesion segmentation methods for Slicer3 EM-segment, ITK itkEMS, ITK lesion segmentation, and Slicer3 manual tracing ('''Jeremy, Chuck, Vince Magnotta, Kilian/Brad, Marcel''')
 
:** Slicer3 EM-segment Module
 
:** Slicer3 EM-segment Module
:*** Currently has a bug that does not permit 3 channel segmentation [http://na-mic.org/Mantis/view.php?id=205 Mantis ID#0000205]
+
:*** (Resolved) Currently has a bug that does not permit 3 channel segmentation [http://na-mic.org/Mantis/view.php?id=205 Mantis ID#0000205]
:**** Only using 2 channels such as T1/T2 or T1/FLAIR does not produce sensible/usable results
+
:**** (Resolved) 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. [http://na-mic.org/Mantis/view.php?id=204 Mantis ID#0000204]
+
:*** (Resolved) Does not properly allow user to edit or change weighting of channels, this is crucial for hierarchical lesion classification. [http://na-mic.org/Mantis/view.php?id=204 Mantis ID#0000204]
 +
:*** EMSegment has been run against collected lupus cases.  Results are currently not sensible/usable as of 05/01/2008.
 +
:**** Currently working with Killian on optimizing parameters in EMSegment to improve the lesion segmentation.
 +
:**** Testing parameters and resulting segmentation on collected lupus cases.
 
:** ITK itkEMS stand-alone package
 
:** 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
 
:*** 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
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:**** stage two use bayesian classifier into normal tissue or lesion using results of stage one and co-reigstered Flair
 
:**** stage two use bayesian classifier into normal tissue or lesion using results of stage one and co-reigstered Flair
 
:***** current results of this method as of 3/17/2008 are shown [[DBP2:MIND:itkBayesianLesion|here]]
 
:***** current results of this method as of 3/17/2008 are shown [[DBP2:MIND:itkBayesianLesion|here]]
 +
:***** This method has been run against all cases as of 05/01/08.  Currently working with Vince Magnotta to improve the performance.
 
:** Slicer3 Manual Tracing
 
:** 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
 
:*** Gasparovic has manually traced all tutorial cases with lesions using T2/Flair images following tracing guidelines and a qualitative neuroradiological review report

Revision as of 15:50, 1 May 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 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 EM-segment Module (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 to the scientific community
    • 5 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 so that users may compare their results with those of the tutorial

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
  • 3/17/2008 complete lesion segmentation methods for Slicer3 EM-segment, ITK itkEMS, ITK lesion segmentation, and Slicer3 manual tracing (Jeremy, Chuck, Vince Magnotta, Kilian/Brad, Marcel)
    • Slicer3 EM-segment Module
      • (Resolved) Currently has a bug that does not permit 3 channel segmentation Mantis ID#0000205
        • (Resolved) Only using 2 channels such as T1/T2 or T1/FLAIR does not produce sensible/usable results
      • (Resolved) Does not properly allow user to edit or change weighting of channels, this is crucial for hierarchical lesion classification. Mantis ID#0000204
      • EMSegment has been run against collected lupus cases. Results are currently not sensible/usable as of 05/01/2008.
        • Currently working with Killian on optimizing parameters in EMSegment to improve the lesion segmentation.
        • Testing parameters and resulting segmentation on collected lupus cases.
    • 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
      • 3/17/2008 update, marcel built a 64-bit linux version that appears to run successfully, current results are are shown here
    • ITK lesion classification stand-alone 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
          • current results of this method as of 3/17/2008 are shown here
          • This method has been run against all cases as of 05/01/08. Currently working with Vince Magnotta to improve the performance.
    • 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 ITK-based lesion analysis algorithm/method (EM-segment, ITK itkEMS, ITK lesion segmentation) 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)
  • 6/15/2008 functioning prototype version of lesion analysis Slicer3 Module complete (Mark Scully, Steve)
  • Tutorial and Data-sharing
  • 6/20/2008 present tutorial to 2008 NA-MIC programming week (Mark Scully, Jeremy, Sonja)
    • A logical project for programming week for Jeremy and Sonja to finish public version of tutorial
  • 7/1/2008 make data sets and tutorial available to the scientific community (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?

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