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
- BRAINS2 has AIR package wrapped
Lesion segmentation
A number of algorithms for fully or semi-automated lesion analysis will be evaluated. These include:
- Tools developed at UNC known as itkEMS Compare Lesion Analysis Tools (Marcel)
- EM-segment (Sandy Wells)
- BRAINS2 (Magnotta)
- Manual tracing by clinically trained rater
Lesion Localization
- Slicer has tools for labeling white matter lesions and summarizing their anatomical location
- BRAINS2 has tools for creating masks for white matter lesions and summarizing their anatomical location
Lesion Load Measurement
- Slicer 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 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 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 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
- 3/31/2008 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
- we have tried EM-Segment
- 3/31/2008 complete lesion segmentation methods for EM-segment, BRAINS2, manual, UNC packages (Jeremy, Chuck, Vince Magnotta, Kilian/Brad, Marcel)
- 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)
- 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)
- 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)
- 1/6/2008 Slicer3 Lesion Analysis Module that handles co-registration of T1, T2, and Flair (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?
- If we submit SFN abstract, we can advertise the availability during SFN Conference in November 2008
- 6/20/2008 present tutorial to 2008 NA-MIC programming week (Mark Scully, Jeremy, Sonja)
- 7/1/2008 make data sets and tutorial available to the public (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