2008 Core 1 Core 3 mtg:notes
Core 3 Presentations
9:30 B&W/Harvard Marek Kubicki, Core 3 Talk. Slides. Stochastic Tractography
- 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
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
- 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.
- 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
- some registration involved
- 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
- 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