Difference between revisions of "Modules:PlastimatchXFORMWARP"

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===Module Description===
 
===Module Description===
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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.
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This is the module for warping image volumes with transforms.  It allows you to select B-spline deformable registration transform (B-spline coefficients) or vector field directrly from MRML tree or from file and use it to warp images, structure sets and doses.
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'''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.
 
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'''Note''': Because DICOM-RT structures are specified as polylines, there is a small loss of fidelity when they are converted into rasterized volumes.
 
  
 
== Usage ==
 
== Usage ==
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|[[Image:plastimatch_dicomrt_tutorial_ppt.png|thumb|280px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1568/3D_Slicer_Plastimatch_DICOM_RT_Tutorial_2010_12_28.pdf Download tutorial (PDF)]]]
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|[[Image:3D_Slicer_Plastimatch_Dose_Warping_Tutorial.png|thumb|280px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1831/3D_Slicer_Plastimatch_Dose_Warping_Tutorial.ppt Download tutorial (PPT)]]]
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|[[Image:plastimatch_dicomrt_ss.png|thumb|230px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/934/chest-phantom-dicomrt-xio-4.33.02.tar.gz (Download tutorial data)]]]
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|[[Image:popi-dose.png|thumb|420px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (Download tutorial data)]]]
 
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* '''Input/Output panel:'''
 
* '''Input/Output panel:'''
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** '''Input DICOM directory:'''  Here you choose any file in the directory which contains the DICOM-RT data.
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** '''Input Volume:'''  Here you choose the volume which will be warped.
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** '''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.
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** '''Input transform (MRML):''' Here you choose the transform from MRML tree.
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** '''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".
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** '''Input transform (file):''' Here you choose the transform from file (type the full path).
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** '''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".
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** '''Output Volume:''' Here you choose where to put the output volume.  Unless you want to replace an existing volume, you should choose "Create New Volume".
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** '''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".
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|[[Image:panel.png|thumb|280px|User Interface]]
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|[[Image:plastimatch_dicomrt_gui.png|thumb|280px|User Interface]]
 
 
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Latest revision as of 16:47, 2 June 2011

Home < Modules:PlastimatchXFORMWARP

Return to Slicer 3.6 Documentation


Plastimatch > Warping with transform

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 module for warping image volumes with transforms. It allows you to select B-spline deformable registration transform (B-spline coefficients) or vector field directrly from MRML tree or from file and use it to warp images, structure sets and doses.

Usage

Tutorials

Download tutorial (PPT)
(Download tutorial data)

Quick Tour of Features and Use

  • Input/Output panel:
    • Input Volume: Here you choose the volume which will be warped.
    • Input transform (MRML): Here you choose the transform from MRML tree.
    • Input transform (file): Here you choose the transform from file (type the full path).
    • Output Volume: Here you choose where to put the output volume. 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

Usability issues

Please report usability issues to the bug tracker.

Source code & documentation

We recommended to download the latest source code from subversion:

Documentation:

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.
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