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
- ITK has mutual information registration
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)
- ITK K Nearest Neighbor classification based on the work of Anabeek, et al
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
- 10 Externally sharable T1,T2,Flair,Lesion Map data-sets (NIFTI format) will be made available to the scientific community
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
- collected 2 patients and 3 controls so far
- 10/15/2007 T1, T2, FLAIR optimized sequences for Siemens 3T Trio Tim scanner (Jeremy, Bruce, Chuck)
- 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
- 1/31/2008 optimized mutual information registration for clinical sequences and optimized 3T sequences (Jeremy)
- 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. Segmentations have improved but are still unusable as of 08/14/2008.
- Currently working with Killian on optimizing parameters in EMSegment to improve the lesion segmentation.
- Testing parameters and resulting segmentation on collected lupus cases.
- (Resolved) Currently has a bug that does not permit 3 channel segmentation Mantis ID#0000205
- 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.
- As of 08/14/2008, currently running a modified version of Vince's classifier that has been improved by replacing intensity thresholding with joint histogram feature vector occurrence thresholding.
- Vince Magnotta has develop an ITK-based 2 stage lesion segmentation method
- ITK K Nearest Neighbor Classifier
- Mark Scully is currently implementing a K-NN lesion classifier using ITK.
- This approach allows for on the fly additions to the classification model.
- The same segmentation approach is applicable to multiple lesion types.
- The resulting label map contains the percent likelihood that a given voxel is a lesion. This allows the clinician to adjust the thresholding to match their preference.
- Mark Scully is currently implementing a K-NN lesion classifier using ITK.
- 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
- Gasparovic has manually traced all tutorial cases with lesions using T2/Flair images following tracing guidelines and a qualitative neuroradiological review report
- Slicer3 EM-segment Module
- 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)
- 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)
- 8/14/2008 submit manuscript on the lesion segmentation methods as applied to MS lesions for MICCAI 2008. (Mark, Jeremy, Chuck, Vince Magnotta)
- 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)
- 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)
- 08/01/2008 currently locates all independent lesion clusters and identifies the anatomical regions, provided by a registered atlas, that the lesions overlap.
- 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)
- 8/14/2008 in the process of creating a module that "chains" together all of the steps in the lesion segmentation analysis pipeline.
- 1/6/2008 Slicer3 Lesion Analysis Module that handles co-registration of T1, T2, and Flair (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?
- If we submit SFN abstract, we can advertise the availability during SFN Conference in November 2008
- 10/15/2008 In the process of making the tutorial data available using XNAT.
- 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