Slicer Wiki - User contributions [en]

Documentation/4.0

2011-11-23T21:09:39Z

Kedar p: /* Converters */

__NOTOC__


[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]

=Table of Content=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
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===Slicer Application===
----
<big>'''
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]] (Wendy Plesniak)

*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)

*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]] (Steve Pieper)

*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)


*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]] (Curtis Lisle)'''
</big>

===Mailing Lists===
----
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]



|bgcolor="#CCCCCC"|
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===Module Categories ===
----
<big>'''
* [[#Core Modules|Core Modules]]
* [[#Wizards|Wizards]]
* [[#Informatics|Informatics]]
* [[#Registration|Registration]]
* [[#Segmentation|Segmentation]]
* [[#Quantification|Quantification]]
* [[#Diffusion|Diffusion]]
* [[#IGT|IGT]]
* [[#Filtering|Filtering]]
* [[#Surface Models|Surface Models]]
* [[#Converters|Converters]]
* [[#Endoscopy|Endoscopy]]
* [[#Developer Tools|Developer Tools]]
* [[#Legacy|Legacy]]
* [[#Utilities|Utility]]
</big>
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===Miscellaneous===
----


* [[Slicer4:VisualBlog|Visual blog]]
: Set of screenshots showing Slicer in action.


* [[Documentation/4.0/Training|Training pages]]
: Information on how to use Slicer {{documentation/version}}

* [[Documentation/{{documentation/version}}/FAQ|FAQ]]
: Set of common questions/answers

===Developers Corner===
----
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]
: Handy Developer Info
|}

=General Information=
{|width="100%"
|rowspan="3"|
{{Infobox
|name = 3D Slicer {{documentation/version}}
|above = 3D Slicer
|abovestyle =

|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]
|imagestyle =
|headerstyle = background:#E7DCC3;
|labelstyle =
|datastyle =

|header1 = Description
|label1 =
|data1 =
|header2 =
|label2 =
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.
|header3 =
|label3 =
|data3 = Free and extensible open source package.
|header4 =
|label4 = Multi-platform
|data4 = Linux, MacOSX, Windows
|header5 =
|label5 = Version
|data5 = {{documentation/version}}
|header6 =
|label6 = License
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]
}}

|align="center"|
[[{{collaborator|logo|slicer4}}|x300px]]
|-
|
{{ombox
|type=content
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement page]] for more details. The community contributing to Slicer {{documentation/version}} is [[Documentation/{{documentation/version}}/Acknowledgment Team|acknowledged here]].
}}
|-
|
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}
|}

=Requirements for Modules=
* The module is '''feature complete''', i.e. it does everything that it advertises
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* The module is fully documented. [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Template]] and [[Documentation/{{documentation/version}}/HowTo|How-to]] for the end user documentation.
* The module complies with [[Documentation-Rons-Rules-For-Tools|Rons rules for tool]] and the style guide lines, including [[Slicer3:Human_Interface_and_Style_Guide_for_Developers#Colors:_application_palettes|color palette]].
* Use logos listed in the [[Template:Collaborator|Collaborators Template]].

=Modules by Category=
==Core Modules==
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak) [[image:UnderConstruction.png|tumb|10px]]

==Wizards==
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov) [[image:UnderConstruction.png|tumb|10px]]

==Informatics==
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)

==Registration==
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
*Specialized
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**Vector Demon Registration (Hans Johnson)

==Segmentation==
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Specialized
**EMSegment Command-line (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]

==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Tractography
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Utilities
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]

==IGT==

==Filtering==
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Resample Tools
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Arithmetic
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Morphology
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Surface Models==
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Label Map Smoothing
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]

==Converters==
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller)
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Endoscopy==
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]
*Module Template
*Multiple Models Example
*Performance Tests
*Tractography

==Legacy==
*Converters
**BSpline to Deformation Field
*Diffusion
**Denoising
***Unbiased Non Local Means Filter for DWI
*Filtering
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
**Resample Scalar Volume
*Registration
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]
**Nonrigid BSpline Registration
**Expert Automated Registration
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]
**Robust Multiresolution Affine Registration
*Segmentation
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]

==Utilities==
*Transform MRML Files to NewSegmenter Standard

=Extensions=

'''Introduction'''

* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions.
* In case of problems with extensions, please talk directly to the developers of the extensions.
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.

==Collections==
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.

{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! Thumbnail
! Name
! Short Description
! Maturity
! Slicer License
! Search terms
! Contact Information
|-
| 1
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyCollection
| This is a collection of extensions that will do something miraculous with your images
| [[File:StableExtensionIcon.png|80px]]
| [[File:SlicerLicenseIcon.png|80px]]
| segmentation, level set
| my-email at mit.edu
|-
|}

==Table Of Extensions==
{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! Thumbnail
! Name
! Short Description
! Maturity
! Slicer License
! Search terms
! Contact Information
|-
| 1
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyExtension
| This is an extension that will do something wonderful with your data
| [[File:ExperimentalExtensionIcon.png|80px]]
| [[File:NoSlicerLicenseIcon.png|80px]]
| filter, anisotropic
| my-email at gmail.com
|-
| 2
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyExtension
| This is an extension that will do something miraculous with your images
| [[File:StableExtensionIcon.png|80px]]
| [[File:SlicerLicenseIcon.png|80px]]
| segmentation, level set
| my-email at mit.edu
|-
|}

'''Caption for the table of extensions'''
<gallery heights="50px" perrow="4">
Image:SlicerLicenseIcon.png‎| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess) Use with care Might not work all the time Might not be available for all platforms
Image:StableExtensionIcon.png|Stable Full documentation Works as advertised Compiles on all supported platforms Email support works
</gallery>

Documentation/4.0

2011-11-23T21:09:23Z

Kedar p: /* Filtering */

__NOTOC__


[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]

=Table of Content=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|

===Slicer Application===
----
<big>'''
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]] (Wendy Plesniak)

*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)

*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]] (Steve Pieper)

*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)


*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]] (Curtis Lisle)'''
</big>

===Mailing Lists===
----
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]



|bgcolor="#CCCCCC"|
|valign="top"|

===Module Categories ===
----
<big>'''
* [[#Core Modules|Core Modules]]
* [[#Wizards|Wizards]]
* [[#Informatics|Informatics]]
* [[#Registration|Registration]]
* [[#Segmentation|Segmentation]]
* [[#Quantification|Quantification]]
* [[#Diffusion|Diffusion]]
* [[#IGT|IGT]]
* [[#Filtering|Filtering]]
* [[#Surface Models|Surface Models]]
* [[#Converters|Converters]]
* [[#Endoscopy|Endoscopy]]
* [[#Developer Tools|Developer Tools]]
* [[#Legacy|Legacy]]
* [[#Utilities|Utility]]
</big>
|bgcolor="#CCCCCC"|
|valign="top"|

===Miscellaneous===
----


* [[Slicer4:VisualBlog|Visual blog]]
: Set of screenshots showing Slicer in action.


* [[Documentation/4.0/Training|Training pages]]
: Information on how to use Slicer {{documentation/version}}

* [[Documentation/{{documentation/version}}/FAQ|FAQ]]
: Set of common questions/answers

===Developers Corner===
----
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]
: Handy Developer Info
|}

=General Information=
{|width="100%"
|rowspan="3"|
{{Infobox
|name = 3D Slicer {{documentation/version}}
|above = 3D Slicer
|abovestyle =

|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]
|imagestyle =
|headerstyle = background:#E7DCC3;
|labelstyle =
|datastyle =

|header1 = Description
|label1 =
|data1 =
|header2 =
|label2 =
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.
|header3 =
|label3 =
|data3 = Free and extensible open source package.
|header4 =
|label4 = Multi-platform
|data4 = Linux, MacOSX, Windows
|header5 =
|label5 = Version
|data5 = {{documentation/version}}
|header6 =
|label6 = License
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]
}}

|align="center"|
[[{{collaborator|logo|slicer4}}|x300px]]
|-
|
{{ombox
|type=content
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement page]] for more details. The community contributing to Slicer {{documentation/version}} is [[Documentation/{{documentation/version}}/Acknowledgment Team|acknowledged here]].
}}
|-
|
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}
|}

=Requirements for Modules=
* The module is '''feature complete''', i.e. it does everything that it advertises
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* The module is fully documented. [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Template]] and [[Documentation/{{documentation/version}}/HowTo|How-to]] for the end user documentation.
* The module complies with [[Documentation-Rons-Rules-For-Tools|Rons rules for tool]] and the style guide lines, including [[Slicer3:Human_Interface_and_Style_Guide_for_Developers#Colors:_application_palettes|color palette]].
* Use logos listed in the [[Template:Collaborator|Collaborators Template]].

=Modules by Category=
==Core Modules==
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich)
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak) [[image:UnderConstruction.png|tumb|10px]]

==Wizards==
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov) [[image:UnderConstruction.png|tumb|10px]]

==Informatics==
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)

==Registration==
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
*Specialized
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**Vector Demon Registration (Hans Johnson)

==Segmentation==
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl)
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Specialized
**EMSegment Command-line (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]

==Quantification==
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)

==Diffusion==
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Tractography
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
*Utilities
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]

==IGT==

==Filtering==
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Resample Tools
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Arithmetic
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Denoising
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Morphology
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Surface Models==
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*Label Map Smoothing
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]

==Converters==
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]

==Endoscopy==
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]
*Module Template
*Multiple Models Example
*Performance Tests
*Tractography

==Legacy==
*Converters
**BSpline to Deformation Field
*Diffusion
**Denoising
***Unbiased Non Local Means Filter for DWI
*Filtering
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]
**Resample Scalar Volume
*Registration
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]
**Nonrigid BSpline Registration
**Expert Automated Registration
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]
**Robust Multiresolution Affine Registration
*Segmentation
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]

==Utilities==
*Transform MRML Files to NewSegmenter Standard

=Extensions=

'''Introduction'''

* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions.
* In case of problems with extensions, please talk directly to the developers of the extensions.
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.

==Collections==
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.

{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! Thumbnail
! Name
! Short Description
! Maturity
! Slicer License
! Search terms
! Contact Information
|-
| 1
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyCollection
| This is a collection of extensions that will do something miraculous with your images
| [[File:StableExtensionIcon.png|80px]]
| [[File:SlicerLicenseIcon.png|80px]]
| segmentation, level set
| my-email at mit.edu
|-
|}

==Table Of Extensions==
{| class="wikitable sortable labelpage labelpagetable" border="1"
|-
! id
! Thumbnail
! Name
! Short Description
! Maturity
! Slicer License
! Search terms
! Contact Information
|-
| 1
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyExtension
| This is an extension that will do something wonderful with your data
| [[File:ExperimentalExtensionIcon.png|80px]]
| [[File:NoSlicerLicenseIcon.png|80px]]
| filter, anisotropic
| my-email at gmail.com
|-
| 2
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]]
| MyExtension
| This is an extension that will do something miraculous with your images
| [[File:StableExtensionIcon.png|80px]]
| [[File:SlicerLicenseIcon.png|80px]]
| segmentation, level set
| my-email at mit.edu
|-
|}

'''Caption for the table of extensions'''
<gallery heights="50px" perrow="4">
Image:SlicerLicenseIcon.png‎| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess) Use with care Might not work all the time Might not be available for all platforms
Image:StableExtensionIcon.png|Stable Full documentation Works as advertised Compiles on all supported platforms Email support works
</gallery>

Documentation/4.0/Modules/GrayscaleFillHoleImageFilter

2011-11-23T21:06:15Z

Kedar p:

File:DWIDicomToNrrdGUI.png

2011-11-23T20:27:01Z

Kedar p: uploaded a new version of "File:DWIDicomToNrrdGUI.png": GUI grabbed from Slicer4.

Documentation/4.0/Modules/DicomToNrrdConverter

2011-11-21T21:50:27Z

Kedar p:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Jim Miller, GE 
Contact: Jim Miller <email>millerjv@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:GE-logo.png|GE
|Image:Itk-logo.jpg|Itk
|Image:NAMIC 380x463.jpg|NA-MIC
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}} }}

{{documentation/{{documentation/version}}/module-section|Use Cases}}
This module is typically used as the first step in diffusion weighted image analysis and tractography to convert diffusion weighted images in Dicom format into Nrrd format, which is recognized by Slicer4 as a legitimate diffusion weighted volume.

In the recent development, it is extended to act as a dicom series to nrrd file converted for non-diffusion-weighted images as well.

Supported DWI formats:

*Philips scanner/software version combinations:
**Achieva 2.1.3.6
**Achieva 2.5.3.0
**Achieva 2.5.3.3
**Achieva 2.6.1.0
**Acheiva 2.6.3.4
**Intera 2.1.3.6
**Intera 2.6.3.5
*Siemens
**Trio B13
**Trio B15
**Trio B17
**Verio B15V
*GE
**SIGNA HDx14.0
**SIGNA HDxt 15.0
**DVMR 20.0M4
**DVMR 20.1

{{documentation/{{documentation/version}}/module-section|Usage}}
A command line example for running the module is:

<pre>
DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr
</pre>
The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the '''smallGradientThreshold''' flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient vectors whose magnitudes were unusually small in Siemens Trio Tim B13 data due to incorrect metadata for diffusion gradient vector coordinate entries in the DICOM header public element tags.

'''For Siemens data:''' In event of incorrect metadata for diffusion gradient vector coordinates in the DICOM header public element tags, please set the '''useBMatrixGradientDirections''' flag. When the useBMatrixGradientDirections flag is set, gradient direction coordinates and b values are derived from the '''bMatrix''' DICOM header private element tag for each gradient. In Siemens DWI data, the b matrix elements are the product of the b value and unit gradient direction vector (column vector) multiplied by the transpose of the unit gradient direction vector. Therefore, for a given gradient direction, the unit gradient direction vector coordinates are the first column of the 3x3 unitary matrix from a singular value decomposition of its b matrix, while the b value is the trace of its b matrix.

{{documentation/{{documentation/version}}/module-section|Panels}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}} }}
{|
|[[Image:DWIDicomToNrrdGUI.png|thumb|280px|Screenshot of the UI]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}}
}}
}}


{{documentation/{{documentation/version}}/module-footer|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}}
}}
}}

Documentation/4.0/Modules/DicomToNrrdConverter

2011-11-21T21:04:19Z

Kedar p:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Jim Miller, GE 
Contact: Jim Miller <email>millerjv@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:GE-logo.png|GE
|Image:Itk-logo.jpg|Itk
|Image:NAMIC 380x463.jpg|NA-MIC
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}} }}

{{documentation/{{documentation/version}}/module-section|Use Cases}}
This module is typically used as the first step in diffusion weighted image analysis and tractography to convert diffusion weighted images in Dicom format into Nrrd format, which is recognized by Slicer3 as a legitimate diffusion weighted volume.

In the recent development, it is extended to act as a dicom series to nrrd file converted for non-diffusion-weighted images as well.

Supported DWI formats:

*Philips scanner/software version combinations:
**Achieva 2.1.3.6
**Achieva 2.5.3.0
**Achieva 2.5.3.3
**Achieva 2.6.1.0
**Acheiva 2.6.3.4
**Intera 2.1.3.6
**Intera 2.6.3.5
*Siemens
**Trio B13
**Trio B15
**Trio B17
**Verio B15V
*GE
**SIGNA HDx14.0
**SIGNA HDxt 15.0
**DVMR 20.0M4
**DVMR 20.1

{{documentation/{{documentation/version}}/module-section|Usage}}
A command line example for running the module is:

<pre>
DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr
</pre>
The module is currently set to quit and alert the user of gradients whose magnitudes are unreasonably small (greater than 0 and less than the smallGradientThreshold) via the '''smallGradientThreshold''' flag (default value for smallGradientThreshold: 0.2). This flag was created after encountering gradient vectors whose magnitudes were unusually small in Siemens Trio Tim B13 data due to incorrect metadata for diffusion gradient vector coordinate entries in the DICOM header public element tags.

'''For Siemens data:''' In event of incorrect metadata for diffusion gradient vector coordinates in the DICOM header public element tags, please set the '''useBMatrixGradientDirections''' flag. When the useBMatrixGradientDirections flag is set, gradient direction coordinates and b values are derived from the '''bMatrix''' DICOM header private element tag for each gradient. In Siemens DWI data, the b matrix elements are the product of the b value and unit gradient direction vector (column vector) multiplied by the transpose of the unit gradient direction vector. Therefore, for a given gradient direction, the unit gradient direction vector coordinates are the first column of the 3x3 unitary matrix from a singular value decomposition of its b matrix, while the b value is the trace of its b matrix.

{{documentation/{{documentation/version}}/module-section|Panels}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}} }}
{|
|[[Image:DWIDicomToNrrdGUI.png|thumb|280px|Screenshot of the UI]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}}
}}
}}


{{documentation/{{documentation/version}}/module-footer|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}}
}}
}}

Documentation/4.0/Modules/DicomToNrrdConverter

2011-11-21T20:59:37Z

Kedar p:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Jim Miller, GE 
Contact: Jim Miller <email>millerjv@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:GE-logo.png|GE
|Image:Itk-logo.jpg|Itk
|Image:NAMIC 380x463.jpg|NA-MIC
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}} }}

{{documentation/{{documentation/version}}/module-section|Use Cases}}
This module is typically used as the first step in diffusion weighted image analysis and tractography to convert diffusion weighted images in Dicom format into Nrrd format, which is recognized by Slicer3 as a legitimate diffusion weighted volume.

In the recent development, it is extended to act as a dicom series to nrrd file converted for non-diffusion-weighted images as well.

Supported DWI formats:

*Philips scanner/software version combinations:
**Achieva 2.1.3.6
**Achieva 2.5.3.0
**Achieva 2.5.3.3
**Achieva 2.6.1.0
**Acheiva 2.6.3.4
**Intera 2.1.3.6
**Intera 2.6.3.5
*Siemens
**Trio B13
**Trio B15
**Trio B17
**Verio B15V
*GE
**SIGNA HDx14.0
**SIGNA HDxt 15.0
**DVMR 20.0M4
**DVMR 20.1


{{documentation/{{documentation/version}}/module-section|Panels}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}} }}
{|
|[[Image:DWIDicomToNrrdGUI.png|thumb|280px|Screenshot of the UI]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}}
}}
}}


{{documentation/{{documentation/version}}/module-footer|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}}
}}
}}

Documentation/4.0/Modules/DicomToNrrdConverter

2011-11-21T20:57:27Z

Kedar p:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Jim Miller, GE 
Contact: Jim Miller <email>millerjv@ge.com</email> 
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|Image:GE-logo.png|GE
|Image:Itk-logo.jpg|Itk
|Image:NAMIC 380x463.jpg|NA-MIC
}}
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{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}} }}

{{documentation/{{documentation/version}}/module-section|Use Cases}}
This module is typically used as the first step in diffusion weighted image analysis and tractography to convert diffusion weighted images in Dicom format into Nrrd format, which is recognized by Slicer3 as a legitimate diffusion weighted volume.

In the recent development, it is extended to act as a dicom series to nrrd file converted for non-diffusion-weighted images as well.

{{documentation/{{documentation/version}}/module-section|Supported DWI formats}}

*Philips scanner/software version combinations:
**Achieva 2.1.3.6
**Achieva 2.5.3.0
**Achieva 2.5.3.3
**Achieva 2.6.1.0
**Acheiva 2.6.3.4
**Intera 2.1.3.6
**Intera 2.6.3.5
*Siemens
**Trio B13
**Trio B15
**Trio B17
**Verio B15V
*GE
**SIGNA HDx14.0
**SIGNA HDxt 15.0
**DVMR 20.0M4
**DVMR 20.1


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module

{{documentation/{{documentation/version}}/module-section|Panels}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}} }}
{|
|[[Image:DWIDicomToNrrdGUI.png|thumb|280px|Screenshot of the UI]]
|}

{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|15308}}
}}
}}


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Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter

2011-11-21T20:51:02Z

Kedar p:

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website]. 
Author: Jim Miller, GE 
Contact: Jim Miller <email>millerjv@ge.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|Image:GE-logo.png|GE
|Image:Itk-logo.jpg|Itk
|Image:NAMIC 380x463.jpg|NA-MIC
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }}


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:

* Use Case 1:

{{documentation/{{documentation/version}}/module-section|Usage}}
GrayscaleGrindPeakImageFilter.exe
[--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--] [--version] [-h] <std::string>
<std::string>
Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume to be filtered

<std::string>
(required) Output filtered


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Links to tutorials that use this module


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Point to other modules that have similar functionality


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=
{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}}
}}
}}


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{{documentation/{{documentation/version}}/module-category|xmlurl=
{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}}
}}
}}

Documentation/4.0/Modules/GrayscaleFillHoleImageFilter

2011-11-21T20:49:00Z

Kedar p: