2008 Core 1 Core 3 mtg:notes

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)