View source for Modules:Plastimatch

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__NOTOC__
===Plastimatch===

{|
|[[Image:plastimatch_image_1.png|thumb|280px|Before Registration]]
|[[Image:plastimatch_image_2.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: Greg Sharp, Department of Radiation Oncology, Massachusetts General Hospital (gcsharp@partners.org)
* Web page: http://plastimatch.org

===Module Description===

== Usage ==

===Tutorials===

{|
|[[Image:plastimatch_tutorial_ppt.png|thumb|280px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1023/3D_Slicer_Plastimatch_Registration_Tutorial.ppt Download tutorial]]]
|[[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]]]
|}

===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.
** '''Cost Function:''' Here you can choose either Mean-squared error (MSE) for unimodal registration, or Mutual Information (MI) for multimodal registration.
** '''Hardware:''' Here you can choose either GPU for CUDA-accelerated registration, or CPU for multicore-accelerated registration.
* '''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.
** '''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]]
|}

== 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, 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.