Project4
From CVRG Wiki
Contents |
Project 4: Grid-Tools for Cardiac Computational Anatomy
Introduction
- Project Investigators: Michael I. Miller (PI-JHU) and J. Tilak Ratnanather (JHU)
- Overview: Project 4 will deliver grid-enabled cardiac computational anatomy tools developed in Project 3 to the user community. This work will be performed in close collaboration with the UCSD team leading overall CVRG Portal development in Project 1 Aim 1D.
- Aim 4A: Implement de-identification and anonymization algorithms so that clinical imaging data will conform to privacy (HIPAA and IRB) requirements.
- Aim 4B: Working with the UCSD team of Project 1, use BioPORTAL to deploy a web-portal for defining landmarks on cardiac structures so that shape and motion analyses (Aim 4C) can be made with reference to a common coordinate system.
- Aim 4C: Working with the UCSD team of Project 1, use BioPORTAL to deploy a web-portal for shape and motion analysis of cardiac structures so that shape and motion features may be computed and uploaded as derived data for subsequent analysis in Project 5
- Aim 4D: Implement visualization modules for shape and motion analysis of cardiac structures.
Research
Segmentation
Seg3D
- Click here for an Introduction to Seg3D and links to download tools.
- Click here for a Seg3D tutorial with screen shots.
3DSlicer
Click here for information on 3D Slicer (Under construction)
Large Deformation Diffeomorphic Metric Mapping
LDDMM Workflow
The LDDMM Workflow pages provide the LDDMM processing workflow.
Through the used of DiffeoMap, we apply LDDMM.
- Identify images for registration - DiffeoMap Registration Video
- Get email notification that the processing has been completed.
- Apply Deformation - DiffeoMap Apply Deformation Video
HTML canvas
A paper the on use of HTML canvas is now online at http://mathdl.maa.org/mathDL/55/?pa=content&sa=viewDocument&nodeId=3340
Metric Pattern Theory
The updated Metric Pattern Theory course is now at http://cis.jhu.edu/education/introPatternTheory/
Statistics
Statistics provides the R and Matlab code for statistical analysis of velocity vectors.
Software Tools
- DiffeoMap - used for LDDMM processing (https://www.mristudio.org/wiki/user_manual/diffeomap)
- ImageJ - used for segmentation and anonymization
- Example usage http://wiki.cvrgrid.org/index.php/Project4/ImageJ
- DicomBrowser - Alternative anonymization tool
- LONI Debabler - Alternative anonymization tool
- Example usage MESA CAP Image De-Identification
- k-PACS - used to upload/download DICOM data from a DICOM server
