View source for 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.
<br><br>
<b>Contributions:</b> New filters, classes.  Application?<br>
<b>Inputs:</b> a segmentation mask, a mesh 
<b>Outputs:</b> deformation field, transformed image(s)<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>
* Mesh generation. Tetmesh reader / converter?  Use Biomesh3D and bridge to ITK?
* Self-updating transform object
* PETSc & MPI within an ITK filter?

<b>Data:</b>
* ?

== Lesion Sizing Toolkit ==
<b>Contributions:</b> Functioning toolkit.  Possibly new ITK filters classes.  Data.
* Already in ITK as an external module.  Contract is to port to use ITKv4 and distribute.
* Using spatial objects as inputs and outputs <br>
<b>Inputs:</b> DICOM
<b>Outputs:</b> Lesion volume measurements and segmentations.<br>

<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.  e.g. Enhanced canny edge detection

<b>Gaps:</b>
* Representing measures as a concept in ITK

<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>Contributions:</b> New ITK module (particle system), filters, classes.<br>
<b>Inputs:</b> Segmentations
<b>Outputs:</b> Point sets<br>

* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]
* Port significant portions to ITKv4
* New ParticleSystem module.  New ITK filter process objects.
* Generic infrastructure for point-based surface representations
* Cross-sectional and longitudinal analysis

<b>What support is needed?</b>
* Logistics of integration and distribution, including 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)
* Need IRB to release image data

<b>Gaps:</b> 
* Multivariate stats:  Bridge to R for complex statistical analysis without going to file system.  Only implement what is needed for within ITK algorithms.