Slicer Wiki - User contributions [en]

Modules:PlastimatchXFORMWARP

2011-06-02T16:47:46Z

NadyaSh: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===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===

{|
|[[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)]]]
|[[Image:popi-dose.png|thumb|420px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (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".
|[[Image:panel.png|thumb|280px|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:

*[http://forge.abcd.harvard.edu/gf/project/plastimatch/ Project page]
*[http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=AccessInfo 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.

Modules:PlastimatchXFORMWARP

2011-06-02T16:47:28Z

NadyaSh: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===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===

{|
|[[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)]]]
|[[Image:popi-dose.png|thumb|420px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (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".
\|[[Image:panel.png|thumb|280px|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:

*[http://forge.abcd.harvard.edu/gf/project/plastimatch/ Project page]
*[http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=AccessInfo 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.

File:Panel.png

2011-06-02T16:41:48Z

NadyaSh:

Modules:PlastimatchXFORMWARP

2011-06-02T16:41:32Z

NadyaSh: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===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===

{|
|[[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)]]]
|[[Image:popi-dose.png|thumb|420px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (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".
|[[Image:panel.png|thumb|280px|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:

*[http://forge.abcd.harvard.edu/gf/project/plastimatch/ Project page]
*[http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=AccessInfo 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.

Modules:PlastimatchXFORMWARP

2011-06-02T16:33:52Z

NadyaSh: /* Tutorials */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===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===

{|
|[[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)]]]
|[[Image:popi-dose.png|thumb|420px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (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".
|[[Image:plastimatch_dicomrt_gui.png|thumb|280px|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:

*[http://forge.abcd.harvard.edu/gf/project/plastimatch/ Project page]
*[http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=AccessInfo 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.

Modules:PlastimatchXFORMWARP

2011-06-02T16:33:36Z

NadyaSh: /* Tutorials */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===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===

{|
|[[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)]]]
|[[Image:popi-dose.png|thumb|430px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (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".
|[[Image:plastimatch_dicomrt_gui.png|thumb|280px|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:

*[http://forge.abcd.harvard.edu/gf/project/plastimatch/ Project page]
*[http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=AccessInfo 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.

Modules:PlastimatchXFORMWARP

2011-06-02T16:33:24Z

NadyaSh: /* Tutorials */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===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===

{|
|[[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)]]]
|[[Image:popi-dose.png|thumb|400px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (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".
|[[Image:plastimatch_dicomrt_gui.png|thumb|280px|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:

*[http://forge.abcd.harvard.edu/gf/project/plastimatch/ Project page]
*[http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=AccessInfo 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.

File:Popi-dose.png

2011-06-02T16:32:37Z

NadyaSh:

2011-02-14T23:16:28Z

NadyaSh:

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Plastimatch > Landmark-based Registartion===

{|
|[[Image:before_reg.png|thumb|280px|Before Registration]]
|[[Image:after_reg.png|thumb|280px|After Registration]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Plastimatch

===Authors, Collaborators & Contact===
* Authors: See COPYRIGHT.TXT contained within the package
* Contact: Nadya Shusharina, Department of Radiation Oncology, Massachusetts General Hospital (nshsuharina@partners.org)
* Web page: http://plastimatch.org

===Module Description===

This is the plastimatch landmark-based deformable image registration module. The intended application of this method is rapid, interactive correction of registration failures with a small number of mouse clicks. Compared to other landmark-based methods, the plastimatch registration method might offer:

# both local and global registration
# regularization of the deformation field

Examples of how this module is being used:

* Intra-subject registration for adaptive radiotherapy
* Inter-subject registration for automatic segmentation

== Usage ==

===Tutorials===

{|
|[[Image:3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.png|thumb|280px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1622/3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.ppt Download tutorial]]]
|[[Image:fixed.png|thumb|230px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]]]
|}

===Quick Tour of Features and Use===

{|
|
* '''Input/Output panel:'''
** '''Fixed Volume:''' Here you choose the "fixed image", which is the reference image.
** '''Moving Volume:''' Here you choose the "moving image", which will be warped to match the fixed image.
** '''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.
** '''Basis function:''' Here you can choose either tps (thin plate splines), or gauss (Gaussian RBF), or wendland (Wendland RBF).
** '''RBF radius:''' Here you can choose the radius of RBF.
** '''Number of clusters:''' Here you can choose the number of landmark clusters.
** '''Stiffness:''' Here you can choose the regularization parameter.
** '''Default Pixel Value:''' Here you can choose the value for pixels with unknown value.
|[[Image:plastimatch_landmark_gui.png|thumb|280px|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.

* 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:

*[http://forge.abcd.harvard.edu/gf/project/plastimatch/ Project page]
*[http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=AccessInfo 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.
* N. Shusharina, G. Sharp "Landmark-based image registration with analytic regularization", IEEE Trans. Med. Imag., submitted, 2011.

File:Fixed.png

2011-02-14T23:16:02Z

NadyaSh:

File:After reg.png

2011-02-14T23:11:13Z

NadyaSh:

File:Afrer reg.png

2011-02-14T23:10:00Z

NadyaSh: uploaded a new version of "File:Afrer reg.png"

Modules:PlastimatchLANDWARP

2011-02-14T23:07:24Z

NadyaSh:

[[image:Slicer3-6Announcement-v2.png| right |3.6 Icon]]
=Introduction=

3D Slicer is a flexible platform that can be easily extended to enable development of both interactive and batch processing tools for a variety of applications.

3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools. Finally, 3D Slicer is distributed under a non-restrictive BSD license.

The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials and measurement widgets, customized colormaps). To the best of our knowledge, no individual segmentation tool provides such powerful visualization capabilities for the user as 3D Slicer. (These paragraphs were provided by A. Fedorov and C. Lisle)

The 3.6 release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Announcements:Slicer3.6 |3.6 Announcement page]] for a list of those changes. The community contributing to Slicer 3.6 is [[Announcments-3.6-Team|acknowledged here]].

*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].
*For sample data see [[SampleData|here]]
*For documentation on other versions of Slicer see [[Documentation|here]]
*For a [[Slicer-3-6-FAQ|FAQ]] see here
*<big>For an overview on how to load your data, see [[Slicer-3.6-Load-Overview|here]]</big>

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:StereoViewing-3.6 | Setting up and using stereoscopic viewing ]] (Curt Lisle, Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)

=Modules=

==Core==
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
*[http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ '''Registration FAQ''']
*Fast Registration
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust Registration
**[[Modules:RegisterImages-Documentation-3.6|Expert Automated Registration]]: automated registration (rigid to affine to nonrigid) with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
*Brain Only Registration
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along the AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data Registration
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmenter-3.6|EM Segmenter]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching Segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|Robust Statistics Segmentation]] Yi Gao (yigao@gatech.edu).
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).
**[[Modules:GrowCutSegmentation-Documentation-3.6|Grow Cut Segmentation]] (Harini Veeraraghavan)

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]
* DWI Denoising
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
**[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer, C-F Westin)
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
* Diffusion Tensor Utilities
**[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
**[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
* Tractography
**[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich)
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo)
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)
* Pipeline
**[[GTRACT_V4 | GTRACT CLI tools]] (Vincent Magnotta)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov)
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*[[Registration:Resampling|'''Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
**[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
**[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
**[[Modules:ModelTransform-Documentation-3.6|Model Transform]]: "Resample triangulated surface models" (Alex Yarmarkovich)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak)
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Slicer Extensions==

'''Introduction'''

* Slicer Extensions are the "on-ramp" to the Slicer "highway". They provide are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.
*'''While the Slicer license is suggested, it is not required for extensions. Please review the documentation of the extension carefully.'''
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions.
* The version that is available through the extension manager is chosen by the developer of that extension
* Not all extensions are available on all platforms. See here for the [[Documentation-3.6:ExtensionStatus|extension status]].
* In case of problems with extensions, please talk directly to the developers of the extensions.
* Information for developers can be found [[Slicer3:Extensions|here]].

'''Available Extensions'''

* Import/Export
** [[Modules:PlastimatchDICOMRT|Plastimatch > DICOM-RT Import]] Greg Sharp (gcsharp@partners.org).
* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
** [[Modules:SkullStripperModule|SkullStripperModule]] '''(in progress)''' Xiaodong Tao (taox AT research.ge.com).
* Registration
**Robust
*** [[Modules:CMTK|CMTK]] Torsten Rohlfing (torsten@synapse.sri.com) (a.k.a. Computational Morphometry Toolkit)
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch > B-spline deformable registration]] Greg Sharp (gcsharp@partners.org).
*** [[Modules:Plastimatch|Plastimatch > Landmark-based registration]] Nadya Shusharina (nshusharina@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Quantification
** [[Modules:LabelDiameterEstimation-Documentation-3.6|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''
For explanations for developers see [[Slicer3:Extensions| here]]

=Other information=

'''Developer Tools'''
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

'''Non-SPL Supported Compatibility Packages'''
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

'''QA Table'''

[[Slicer-3.6-QA|Slicer 3.6 QA table]]