Summer ITKv4 ClinicalGroupMeetingNotes: Difference between revisions
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== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) == | == 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. | The following is a rough pipeline of the method with proposed classes. | ||
<br><br> | |||
<b>Inputs:</b> a segmentation mask, a mesh<br> | |||
<b>Outputs:</b> deformation field, transformed image(s)<br> | |||
<br> | |||
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. | |||
# 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. | |||
# PBMSolver: PETSc dependence | |||
# ImageWarp: Already in ITK | |||
<b>What support is needed?</b> | |||
* CMake integration w/ PETSc and MPI. Build / distribution issues. | |||
* Further discussion and collaboration with the FEM, registration, and GPU groups. | |||
<b>Gaps:</b> | |||
Gaps: | |||
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK? | * Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK? | ||
* Self-updating transform object | * Self-updating transform object | ||
* PETSc & MPI within an ITK filter? | * PETSc & MPI within an ITK filter? | ||
Data: | <b>Data:</b> | ||
* ? | * ? | ||
== Lesion Sizing Toolkit == | == Lesion Sizing Toolkit == | ||
Inputs: DICOM | <b>Inputs:</b> DICOM | ||
Outputs: Lesion volume measurements and segmentations | <b>Outputs:</b> Lesion volume measurements and segmentations. | ||
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute. | |||
* Using spatial objects as inputs and outputs | * Using spatial objects as inputs and outputs | ||
What support | <b>What support is needed?</b> | ||
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. | * Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection | ||
Gaps: | <b>Gaps:</b> | ||
* Representing measures as a concept in ITK | * 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. | <b>Data:</b> 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 == | |||
<b>Inputs:</b>Segmentations | |||
<b>Outputs:</b>Point sets | |||
* Existing code base mostly ITK | |||
* Port significant portions to ITKv4 | |||
* New ParticleSystem module, new ITK filter process objects. | |||
<b>What support is needed?</b> | |||
* Logistics of integration and distribution, including data. | |||
Data: | <b>Data:</b> | ||
* 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) | * 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 | * Need IRB to release image data | ||
Gaps: | <b>Gaps:</b> | ||
* Multivariate stats | * Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms. | ||
Revision as of 16:56, 27 June 2011
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)
- FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter.
- 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.
- PBMSolver: PETSc dependence
- ImageWarp: Already in ITK
What support is needed?
- CMake integration w/ PETSc and MPI. Build / distribution issues.
- Further discussion and collaboration with the FEM, registration, and GPU groups.
Gaps:
- Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?
- Self-updating transform object
- PETSc & MPI within an ITK filter?
Data:
- ?
Lesion Sizing Toolkit
Inputs: DICOM Outputs: Lesion volume measurements and segmentations.
- Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.
- Using spatial objects as inputs and outputs
What support is 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. e.g. Enhanced canny edge detection
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
Inputs:Segmentations Outputs:Point sets
- Existing code base mostly ITK
- Port significant portions to ITKv4
- New ParticleSystem module, new ITK filter process objects.
What support is needed?
- Logistics of integration and distribution, including data.
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. Only implement what is needed for within ITK algorithms.
