Modules:PlastimatchXFORMWARP - Revision history

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

2011-06-02T16:47:46Z

Quick Tour of Features and Use

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

2011-06-02T16:47:28Z

Quick Tour of Features and Use

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

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Quick Tour of Features and Use

NadyaSh: /* Tutorials */

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Tutorials

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Tutorials

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Tutorials

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Tutorials

NadyaSh: /* Tutorials */

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Tutorials

NadyaSh: /* Module Description */

2011-06-02T15:23:54Z

Module Description

NadyaSh: Created page with 'Return to Slicer 3.6 Documentation NOTOC ===Plastimatch > Warping with transform === == General Information == ===Module Type & Category=== Type: CLI…'

2011-06-02T15:16:02Z

Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Plastimatch > Warping with transform === == General Information == ===Module Type & Category=== Type: CLI…'

New page

[[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 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===

{|
|[[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)]]]
|[[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)]]]
|}

===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<br />
NIH / NCI 6-PO1 CA 21239<br />
Federal share of program income earned by MGH on C06CA059267

Progetto Rocca Foundation<br />
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.

@@ Line 38: / Line 38: @@
 ** '''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]]
+|[[Image:panel.png|thumb|280px|User Interface]]
 |}

@@ Line 25: / Line 25: @@
 {|
 |[[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)]]]
+|[[Image:popi-dose.png|thumb|420px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (Download tutorial data)]]]
 |}

@@ Line 25: / Line 25: @@
 {|
 |[[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)]]]
+|[[Image:popi-dose.png|thumb|430px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (Download tutorial data)]]]
 |}

@@ Line 25: / Line 25: @@
 {|
 |[[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|230px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (Download tutorial data)]]]
+|[[Image:popi-dose.png|thumb|400px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (Download tutorial data)]]]
 |}

@@ Line 24: / Line 24: @@
 {|
-|[[Image:plastimatch_dicomrt_tutorial_ppt.png|thumb|280px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1831/3D_Slicer_Plastimatch_Dose_Warping_Tutorial.ppt Download tutorial (PPT)]]]
+|[[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: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)]]]
+|[[Image:popi-dose.png|thumb|230px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz (Download tutorial data)]]]
 |}

@@ Line 34: / Line 34: @@
+|
 * '''Input/Output panel:'''
-** '''Input DICOM directory:'''  Here you choose any file in the directory which contains the DICOM-RT data.
+** '''Input Volume:'''  Here you choose the volume which will be warped.
-** '''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.
+** '''Input transform (MRML):''' Here you choose the transform from MRML tree.
-** '''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".
+** '''Input transform (file):''' Here you choose the transform from file (type the full path).
-** '''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 Volume:''' Here you choose where to put the output volume.  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]]
 |}

@@ Line 17: / Line 17: @@
 ===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.
+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 ==

Modules:PlastimatchXFORMWARP - Revision history

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

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

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

NadyaSh: /* Tutorials */

NadyaSh: /* Tutorials */

NadyaSh: /* Tutorials */

NadyaSh: /* Tutorials */

NadyaSh: /* Tutorials */

NadyaSh: /* Module Description */

NadyaSh: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Plastimatch > Warping with transform === == General Information == ===Module Type & Category=== Type: CLI…'

NadyaSh: Created page with 'Return to Slicer 3.6 Documentation NOTOC ===Plastimatch > Warping with transform === == General Information == ===Module Type & Category=== Type: CLI…'