Summer ITKv4 ClinicalGroupMeetingNotes
3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration)
The following is a rough pipeline of the method with proposed classes.
Inputs: a segmentation mask, a mesh Outputs: deformation field, transformed image(s)
1) FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. 2) BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version. 3) PBMSolver: PETSc dependence 4) ImageWarp: Already in ITK
Gaps:
- Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?
- Self-updating transform object
- PETSc & MPI within an ITK filter?
What support is needed?
- CMake integration w/ PETSc and MPI. Build / distribution issues.
- Further discussion and collaboration with the FEM, registration, and GPU groups.
Data:
- ?
Lesion Sizing Toolkit
Inputs: DICOM Outputs: Lesion volume measurements and segmentations.
- Already in ITK as an external module. Contract is to reimplement with ITKv4 and distribute.
- Using spatial objects as inputs and outputs
- Should some of these algorithms be migrated into ITK proper? (e.g. enhanced canny edge detection)
What support it needed?
- Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups.
Gaps:
- Representing measures as a concept in ITK
Data: 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.
ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling
Data:
- 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)
- Need IRB to release image data
Gaps:
- Multivariate stats.
- Bridge to R for complex statistical analysis without going to file system.
