Difference between revisions of "Modules:PlastimatchDICOMRT"

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(Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Plastimatch > DICOM-RT Import === {| |thumb|280px|Need Image |[[Image:need_image.…')
 
 
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{|
 
{|
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|[[Image:need_image.png|thumb|280px|Need Image]]
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|[[Image:plastimatch_dicomrt_ss.png|thumb|280px|DICOM-RT Structure Set]]
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|[[Image:need_image.png|thumb|280px|Need Image]]
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|[[Image:plastimatch_dicomrt_dose.png|thumb|280px|DICOM-RT Dose]]
 
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===Module Description===
 
===Module Description===
−
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:
+
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.
−
 
 
−
* 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:
+
'''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.
  
−
* FDK cone-beam CT reconstruction (GPU and multicore accelerated)
+
'''Note''': Because DICOM-RT structures are specified as polylines, there is a small loss of fidelity when they are converted into rasterized volumes.
−
* Digitally reconstructed radiograph (DRR) generation (GPU and multicore accelerated)
 
  
 
== Usage ==
 
== Usage ==
−
 
−
===Use Cases, Examples===
 
−
 
−
Plastimatch contains three separate plugins.  This wiki page documents the automatic B-Spline deformable registration plugin.
 
−
 
−
* Automatic (B-spline) deformable image registration
 
−
Compared to other methods, the plastimatch registration method probably offers (1) superior accuracy for CT-CT registration, and (2) faster results.  However, the plastimatch transform is not compatible within the MRML scene, so you cannot easily use it together with other plugins. 
 
−
 
−
* Manual (landmark) deformable image registration
 
−
If you need to manually adjust your registration results, this is the tool for you!  You can define a small number of corresponding landmarks (as few as one or two) to repair minor misregistrations. 
 
−
However, the plastimatch transform is not compatible within the MRML scene, so you cannot easily use it together with other plugins. 
 
−
 
−
* DICOM-RT structure set import
 
−
This handy plugin will load a DICOM-RT structure set, and render it as a labelmap. 
 
−
 
−
Examples of the module in use:
 
−
 
−
* Intra-subject registration for adaptive radiotherapy
 
−
* Inter-subject registration for automatic segmentation
 
  
 
===Tutorials===
 
===Tutorials===
  
 
{|
 
{|
−
|[[Image:plastimatch_tutorial_ppt.png|thumb|280px|[http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=browse&path=%2F%2Acheckout%2A%2Fplastimatch%2Ftrunk%2Fdoc%2F3D_Slicer_Plastimatch_Registration_Tutorial.ppt Download tutorial]]]
+
|[[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:plastimatch_tutorial_data.png|thumb|230px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1004/rider-lung-images.tar.gz Download tutorial data]]]
+
|[[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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|
 
|
 
* '''Input/Output panel:'''
 
* '''Input/Output panel:'''
−
** '''Fixed Volume:'''  Here you choose the "fixed image", which is the reference image.
+
** '''Input DICOM directory:'''  Here you choose any file in the directory which contains the DICOM-RT data.
−
** '''Moving Volume:''' Here you choose the "moving image", which will be warped to match the fixed image.
+
** '''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 Volume:''' Here you choose where to put the warped image.  You can replace an existing image in the scene, or create a new image.
+
** '''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".
−
** '''Cost Function:''' Here you can choose either Mean-squared error (MSE) for unimodal registration, or Mutual Information (MI) for multimodal registration.
+
** '''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".
−
** '''Hardware:''' Here you can choose either GPU for CUDA-accelerated registration, or CPU for multicore-accelerated registration.
+
** '''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".
−
* '''Stage 0 panel:''' Stage 0 is the a pre-alignment stage, which uses either a translation, rigid transform, or affine transform to make a rough alignment of the moving image to the fixed image.  The default is not to do pre-alignment.  If your images are reasonably well aligned you can keep this option off, which makes plastimatch run faster.  But generally it doesn't hurt to enable Stage 0.
+
|[[Image:plastimatch_dicomrt_gui.png|thumb|280px|User Interface]]
−
** '''Enable Stage 0:'''  Click on this checkbox to enable the pre-alignment stage.
 
−
** '''Image Subsampling Rate:'''  This option is specified as three integers, separated by commas.  It tells plastimatch to subsample the images in the (x,y,z) dimensions by this amount for this stage.  This is one of the methods that plastimatch implements multi-resolution registration. by cascading stages of different subsampling rates.
 
−
** '''Max Iterations:''' This option controls how many iterations of B-spline registration will be run in this stage.  Usually there is no benefit beyond 200 iterations.  Also, there is usually no harm in running extra iterations, except that it takes longer.
 
−
** '''Transformation:''' This option controls whether the pre-alignment uses a translation (3 DOF), a rigid transform (6 DOF), or an affine transform (12 DOF).  Generally speaking, translation is recommended unless the images are extremely different.
 
−
* '''Stage 1 panel:''' Stage 1 is the first stage of non-rigid registration.  The plastimatch plugin will always do at least one non-rigid stage.
 
−
** '''Image Subsampling Rate:''' This option is specified as three integers, separated by commas.  It tells plastimatch to subsample the images in the (x,y,z) dimensions by this amount for this stage.  This is one of the methods that plastimatch implements multi-resolution registration. by cascading stages of different subsampling rates.
 
−
** '''Max Iterations:''' This option controls how many iterations of B-spline registration will be run in this stage.  Usually there is no benefit beyond 200 iterations.  Also, there is usually no harm in running extra iterations, except that it takes longer.
 
−
** '''Grid Spacing:''' The grid spacing parameter is a floating point number which controls the size of the B-spline control grid, in mm.  Larger spacing means a smoother registration, while smaller spacing means a finer registration.
 
−
* '''Stage 2 panel:'''  Stage 2 is an optional second round of non-rigid registration.  If you get good results after stage 1, you might try stage 2 to further improve the results.  However, enabling stage 2 increases the time required to perform the registration.
 
−
** '''Enable Stage 2:'''  Click on this checkbox to enable stage 2.
 
−
** '''Image Subsampling Rate:'''  This option is specified as three integers, separated by commas.  It tells plastimatch to subsample the images in the (x,y,z) dimensions by this amount for this stage.  This is one of the methods that plastimatch implements multi-resolution registration. by cascading stages of different subsampling rates.
 
−
** '''Max Iterations:''' This option controls how many iterations of B-spline registration will be run in this stage.  Usually there is no benefit beyond 200 iterations.  Also, there is usually no harm in running extra iterations, except that it takes longer.
 
−
** '''Grid Spacing:''' The grid spacing parameter is a floating point number which controls the size of the B-spline control grid, in mm.  Larger spacing means a smoother registration, while smaller spacing means a finer registration.
 
−
|[[Image:plastimatch_bspline_gui.png|thumb|380px|User Interface]]
 
 
|}
 
|}
  
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== More Information ==  
 
== 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===
 
===Acknowledgment===
Line 142: Line 116:
 
===References===
 
===References===
  
−
* G Sharp, N Kandasamy, H Singh, M Folkert, "GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration," Physics in Medicine and Biology, 52(19), pp 5771-83, 2007.
 
−
* V Boldea, G Sharp, SB Jiang, D Sarrut, "4D-CT lung motion estimation with deformable registration: Quantification of motion nonlinearity and hysteresis," Medical Physics, 33(3), pp 1008-18, 2008.
 
−
* Z Wu, E Rietzel, V Boldea, D Sarrut, G Sharp, "Evaluation of deformable registration of patient lung 4DCT with sub-anatomical region segmentations," Medical Physics, 35(2), pp 775-81, 2008.
 
 
* 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.
 
* 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.

Latest revision as of 16:58, 28 December 2010

Home < Modules:PlastimatchDICOMRT

Return to Slicer 3.6 Documentation


Plastimatch > DICOM-RT Import

DICOM-RT Structure Set
DICOM-RT Dose

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

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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