2008 Core 1 Core 3 mtg:notes

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Core 3 Presentations

9:30 B&W/Harvard Marek Kubicki, Core 3 Talk. Slides. Stochastic Tractography

Additional discussion:

  • Slicer3 release date? Some question regarding proper handling of coordinate frames in Slicer3.
  • Discussion of registration and existing/needed tools in Slicer 3. Discussion postponed to registration session.
  • Discussion re bias field correction and EM seg -> perhaps moreCore3/Core1 interaction needed

9:50 Queen's U not here yet -> talk postponed

9:50 UNC Rachel Smith talk. Slides. Longitudinal study of brain devel. in autism. Additional discussion:

  • Brief discussion of segmentation methods for brain substructure segmentations
  • Additional clarification/specifics of the status of the processing of datasets
  • Status of Marcel segmentation modules and issues re Core2/1 interaction issues -> Utah (Guido, Marcel) waiting for resolution of some critical Core2 software infrastructure issues e.g. chaining infrastructure design before

they can finalize tools

  • Cortical thickness measurment algorithms-> Advantages/drawbacks of different methods. Guido: we should compare methods and see difference in simpler vs. more complex algorithms. Martin: Core 3 intends to look at this issue
  • Cortical correspondence-> Martin gives update on local correspondence methods status (particle method with freesurfer preprocessing). Issue: Freesurfer not working for pediatric data. Critical Freesurfer functionality will be reimplemented as NAMIC tool

10:20 break

Jeremy Bockholt (DPB lupus)

  • collecting new data/ ongoing clinical study (old data)
  • discussion about how DTI sequences are selected
  • discussion about analysis of lesion growth and identification in follow up images
    • ability to find follow up lesions
    • growth may merge lesions. lesions may disappear. not expected for lesions to move
  • question to test - does lesion information correlate with clinical measures/outcomes
  • Discussion of classification comparison for lesions
  • Comment on the MICCAI workshop on MS lesions segmentation
  • Discussion on methods for segmentation comparison
  • Discussion of commercial tool JIM

Core 1 Presentations

John Melonakos & Yi Gao (segmentation)

  • prostate segmentation (Yi Gao)
    • Extraction of concave valley of prostate for use as landmark in registration
    • Discussion of comparison to UNC work (Steve Pizer's group) on prostate segmentation
    • 3D Ultrasound (raw vs reconstructed)
  • lesion segmentation (John Melonakos)
    • Question on how lesions manifest in DTI images (reduced FA; increased MD)
    • Boundary of CSF around ventricles appears similar to lesion
      • lesions can occur in same region
      • Radiologist heuristic has to do with symmetry to distinguish partial voluming from real lesions
  • tissue classification
  • label space segmentation
    • Question on meaning of binary vectors representation
    • Explanation of LogOdds representation
    • Comment on work on label spaces in volume rendering
  • discussion of tissue labeling versus boundary segmentation
    • itk-snap
    • freesurfer
    • parametrization not available in tissue labeling approaches
    • cortical analysis - thickness and alignment - do we want a surface based approach? hybrid approaches?
    • Integrating DTI into cortical-based analysis frameworks
    • Discussion of how to approach external freely available tools. reimplement in slicer? link to external tools? develop new algorithms?
      • relation to renewal.
      • how core 1 and core 2 interact on this
      • innovation in new algorithm improvement as well as engineering. need to show novelty.
      • validation
        • comparison of methods
        • ground truth - cortical thickness validated by dissection and histology (MGH)
        • reproducibility by making software and data available
  • clinical choice of MR sequences - tools which need special sequences
    • UNC - special sequences needed for pediatric imaging. strong time limitations. optimized contrast for pediatric populations
    • BWH - DTI imaging resolution and effect on distortion (high resolutions needed for smaller sequences)
    • multi-site studies some data had to be rejected due to inconsistent protocols across sites. freesurfer sequence requires special agreement with MGH
    • differences from scanner advancement - 1.5 T vs 3 T and bias field inhomogeneity
    • comment - tools should be independent of choice of pulse sequence.
    • retrospective data from clinical scans. need tools that can handle this
    • arguments need to be made by DBPs with regard to tools being independent of scanner sequences
    • open source tools which can be reengineered for different purposes. namic tools should be be reconfigurable. freesurfer cannot be modified.
    • comment that freesurfer can be used with other pulse sequences with some preprocessing; freesurfer has two components 1) tissue classification 2) surfaces
    • want to be able to mix and match classification, bias field correction, surfaces
    • matching across surfaces

Guido Gerig (DTI)

  • Utah - DTI DICOM issues
    • Oblique slices not recommended
    • Distortion of EPI may lead to desire for oblique slices
  • GA Tech - Tensor reorientation
    • question - tensor invariants instead of reorientation

MIT - stochastic tractography

    • visualization of monte-carlo sampled streamlines
    • what is the level of interest in engineering effort in stochastic tractography? consensus seems to be that it is important
    • what is the analysis on top of stochastic tractography?
      • mask for statistics
    • probability of connection to ROIs
    • multiple connections
    • 5 minute runtime for stochastic tractography
    • not truly MCMC - parameters of tensor are fixed
  • MIT - DTI clustering
    • some registration involved
      • distortion not accounted
      • registration of fibers
  • Utah 1 - EPI correction
    • currently software not available
    • GA tech working on EPI correction with optimal mass transport
  • Utah 1 - volumetric pathway
    • how to determine if path is real? Guaranteed to produce a tract even if none exists. Pathway cost is way of measuring whether patch is meaningful. Similary problem exists in stochastic tractography and GA tech method.
    • probabilistic interpretation of these methods
    • along tract statistics becoming common
  • Population-based analysis
    • MIT/Harvard - arc-length ; pointwise statistics
    • Utah 1 - Arcuate in autism
  • Utah 2 - population based analysis
    • replacement with open source b-spline approach from Serdard & Polina
    • comparison of linear to non-linear alignment
  • Tractography validation
    • What is the outcome?
    • Validation a little early - tools still in development
    • DTI research requires substantial knowledge of DTI and data
    • Project increased discussion among PIs
    • manpower issue
    • NIH pressure to show value added of methods
      • How do we recomend tools for specific problem?
      • Are we close to validation challenge like MICCAI workshop
      • Can we generate synthetic data?
      • need to develop recommendations for usage of methods
      • this is needed for renewal
      • would like input from DBPs on goals for analysis. what would they like to measure?
      • input from animal imaging would be helpful
  • Conclusions
    • Core 2 help needed to integrate tools which work for developers. Would like to transition to users.
    • Do users want multiple tools? How do we decide what to expose to users.
    • NITRC and Slicer as repository of tools
    • Overarching design for recommended default pipeline.
    • Tutorials for specific tools versus tutorial on what methods are available for DTI
    • need to develop pipeline for users
    • Good news - all tools needed for pipeline are available
    • Need way to develop integration