Modules:PlastimatchXFORMWARP

Return to Slicer 3.6 Documentation

General Information

Module Type & Category

Type: CLI

Category: Plastimatch

Authors, Collaborators & Contact

• Authors: See AUTHORS.TXT contained within the package
• Contact: Greg Sharp, Department of Radiation Oncology, Massachusetts General Hospital (gcsharp@partners.org)
• Web page: http://plastimatch.org

Module Description

This is the DICOM / DICOM-RT import module. It allows you to select a directory containing DICOM-RT structure sets and/or dose, which it will convert into 3D Slicer labelmap and/or scalar image. This module also loads the DICOM CT image without requiring the need to use the Slicer volume import wizard.

Note: In a Slicer, a labelmap voxel can only belong to one structure. However, DICOM-RT allows a region to belong to any number of strucutres. Therefore, importing DICOM-RT structure sets as Slicer labelmaps will usually result in a loss of data. This module uses a "last structure wins" strategy for assigning labels to overlapping volumes.

Note: Because DICOM-RT structures are specified as polylines, there is a small loss of fidelity when they are converted into rasterized volumes.

Usage

Tutorials

Download tutorial (PDF)

(Download tutorial data)

Quick Tour of Features and Use

Input/Output panel: Input DICOM directory: Here you choose any file in the directory which contains the DICOM-RT data. Reference Volume (to set size): This is an optional field. But if your dicom directory does not contain a CT, it is required. Here you choose any loaded volume. The import module will create a labelmap at the same resolution and pixel spacing as the reference volume that you choose here. Output Image: Here you choose where to put the output CT image. Unless you want to replace an existing volume, you should choose "Create New Volume". Output Labelmap: Here you choose where to put the output DICOM-RT structure set labelmap. Unless you want to replace an existing volume, you should choose "Create New Volume". Output Dose Image: Here you choose where to put the output DICOM-RT dose image. Unless you want to replace an existing volume, you should choose "Create New Volume".

User Interface

Development

Notes from the Developer(s)

Developer-oriented documentation is found on the plastimatch web site: http://plastimatch.org

Dependencies

This module has no dependencies.

Tests

Plastimatch features approximately 100 test cases.

Known bugs

• http://forge.abcd.harvard.edu/gf/project/plastimatch/tracker/?action=TrackerItemBrowse&tracker_id=450

Usability issues

Please report usability issues to the bug tracker.

• http://forge.abcd.harvard.edu/gf/project/plastimatch/tracker/?action=TrackerItemBrowse&tracker_id=450

Source code & documentation

We recommended to download the latest source code from subversion:

• Project page
• Source download (svn access)

Documentation:

• http://plastimatch.org

More Information

About plastimatch

Plastimatch is an open source software for deformable image registration. It is designed for high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). Software features include:

• B-spline method for deformable image registration (GPU and multicore accelerated)
• Demons method for deformable image registration (GPU accelerated)
• ITK-based algorithms for translation, rigid, affine, demons, and B-spline registration
• Pipelined, multi-stage registration framework with seamless conversion between most algorithms and transform types
• Landmark-based deformable registration using thin-plate splines for global registration
• Landmark-based deformable registration using radial basis functions for local corrections
• Broad support for 3D image file formats (using ITK), including Dicom, Nifti, NRRD, MetaImage, and Analyze
• Dicom and DicomRT import and export
• XiO import and export
• Plugins for 3D Slicer

Plastimatch also features two handy utilities which are not directly related to image registration:

• FDK cone-beam CT reconstruction (GPU and multicore accelerated)
• Digitally reconstructed radiograph (DRR) generation (GPU and multicore accelerated)

Acknowledgment

National Institutes of Health
NIH / NCI 6-PO1 CA 21239
Federal share of program income earned by MGH on C06CA059267

Progetto Rocca Foundation
A collaboration between MIT and Politecnico di Milano

References

• G Sharp et al. "Plastimatch - An open source software suite for radiotherapy image processing," Proceedings of the XVIth International Conference on the use of Computers in Radiotherapy, May, 2010.