Modules:PlastimatchDICOMRT - Revision history

Gregsharp: /* Tutorials */

2010-12-28T16:58:10Z

Tutorials

Gregsharp: /* More Information */

2010-06-08T20:54:18Z

More Information

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

2010-06-08T20:24:41Z

Quick Tour of Features and Use

Gregsharp: /* Module Description */

2010-06-08T20:23:48Z

Module Description

Gregsharp: /* Module Description */

2010-06-08T20:23:27Z

Module Description

Gregsharp: /* Module Description */

2010-06-08T20:17:52Z

Module Description

Gregsharp: /* Plastimatch > DICOM-RT Import */

2010-06-08T20:13:15Z

Plastimatch > DICOM-RT Import

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

2010-06-08T20:13:00Z

Quick Tour of Features and Use

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

2010-06-08T20:11:30Z

Quick Tour of Features and Use

Gregsharp: /* Tutorials */

2010-06-08T20:05:19Z

Tutorials

@@ Line 33: / Line 33: @@
 {|
-|[[Image:plastimatch_dicomrt_tutorial_ppt.png|thumb|280px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1025/3D_Slicer_Plastimatch_DICOM_RT_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)]]]
 |[[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)]]]
 |}

← Older revision		Revision as of 20:54, 8 June 2010
Line 86:		Line 86:

	== 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 46: / Line 46: @@
 ** '''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 labelmap.  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 dose image.  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]]
 |}

@@ Line 24: / Line 24: @@
 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 labelmap, a 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''': 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.

@@ Line 26: / Line 26: @@
 '''Note''': In a Slicer labelmap, a 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.  You may minimizing this effect by creating high resolution lablemaps, such as with 1 mm voxels.
+'''Note''': Because DICOM-RT structures are specified as polylines, there is a small loss of fidelity when they are converted into rasterized volumes.
 == Usage ==

@@ Line 22: / Line 22: @@
 ===Module Description===
-This is the DICOM-RT structure set import module.  It allows you to select a file containing DICOM-RT structure sets, and it creates a 3D Slicer labelmap volume.
+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 labelmap, a 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.

@@ Line 6: / Line 6: @@
 {|
 |[[Image:plastimatch_dicomrt_ss.png|thumb|280px|DICOM-RT Structure Set]]
-|[[Image:plastimatch_dicomrt_dose.png|thumb|280px|DICOM-RT Dose (coming soon)]]
+|[[Image:plastimatch_dicomrt_dose.png|thumb|280px|DICOM-RT Dose]]
 |}

@@ Line 44: / Line 44: @@
 * '''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):''' 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.  This field is required.
+** '''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 Labelmap:''' Here you choose where to put the output labelmap.  Unless you want to replace an existing volume, you should choose "Create New Volume".
 |[[Image:plastimatch_dicomrt_gui.png|thumb|280px|User Interface]]
 |}