Slicer Wiki - User contributions [en]

Modules:BRAINSResample

2010-05-17T18:37:23Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSResample

{|
|[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSResample is a program whose purpose is to resample image volumes to a new resolution, optionally applying a transformation.
== Usage ==
BRAINSResample collects together three common image processing tasks that all involve resampling an image volume: Resampling to a new resolution and spacing, Rigid transformation (using an ITK transform) and Warping (using a deformation field volume).

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

{|
|

*Input Image Files
**Image To Warp: Input Image to transform/warp
**Reference Image: Defines the output space into which Image will be warped
**Deformation Field: Vector volume defining voxel transformation
*Warping Parameters
**Warp By Transform: Filename of BRAINSFit Transfrom file to use in place of deformation field
**Pixel Type: Specifies pixel type for input & output image. "binary" pixel type uses a modified algorithm whereby the image is read as unsigned char voxels, a signed distance map is created, te signed distance map is resampled, and the thresholded image is written to disk.
**Interpolation Mode: Specifies which interpolator is used.
**Invert Linear Transform: Perform transform inversion in ITK physical space before applying linear transform to the image.
*Result File
**Output Image: the input image, transformed/warped and then resampled into the reference image space.
|[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

<!== ===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==
List of all parameters

--outputVolume <std::string>
Resulting deformed image

--useTransformMode <std::string>
This defunct parameter is no longer in service. Now ApplyWarp infers
the transform type from the contents of the .mat file.

--defaultValue <float>
Default voxel value (default: 0)

--invertTransform
Perform transform inversion in itk physical space before applying the
linear transform to the image. (default: 0)

--interpolationMode <NearestNeighbor|Linear|BSpline|WindowedSinc>
Type of interpolation used (default: Linear)

--pixelType <uchar|short|ushort|int|uint|float|binary>
Specifies the pixel type for the input/output images. The 'binary'
pixel type uses a modified algorithm whereby the image is read in as
unsigned char, a signed distance map is created, signed distance map
is resampled, and then a thresholded image of type unsigned char is
written to disk. (default: uchar)

--warpTransform <std::string>
Filename for the BRAINSFit transform used in place of the deformation
field

--deformationVolume <std::string>
Deformation Field

--referenceVolume <std::string>
Reference image defining the output space

--inputVolume <std::string>
Image To Warp

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.
-->

Modules:BRAINSROIAuto-Documentation-3.6

2010-05-07T15:37:03Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSROIAuto

{|
|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSROIAuto is a program whose purpose is to automatically generate a Binary Image (or Mask) to encompass the region in an brain image volume occupied by the brain.
== Usage ==
In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

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

{|
|
*IO Parameters
**Input Image Volume: Image for which mask should be generated
**Output Mask: Output binary image volume, defining the mask.
**Output Image Clipped by ROI: Optional image volume generated by masking the input image with the generated mask.
*Configuration Parameters
**Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.
**Otsu Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.
**Closing Size: The size for the largest void to fill in the mask, in voxels.
**Output Image Pixel Type: the scalar type of the masked output volume.
|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

Modules:BRAINSROIAuto-Documentation-3.6

2010-05-07T15:34:40Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSROIAuto

{|
|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSROIAuto is a program whose purpose is to automatically generate a Binary Image (or Mask) to encompass the region in an brain image volume occupied by the brain.
== Usage ==
In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

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

{|
|
*IO Parameters
**Input Image Volume: Image for which mask should be generated
**Output Mask: Output binary image volume, defining the mask.
**Output Image Clipped by ROI: Optional image volume generated by masking the input image with the generated mask.
*Configuration Parameters
**Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.
**Otsu Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.
**Closing Size: The size for the largest void to fill in the mask, in voxels.
**Output Image Pixel Type: the scalar type of the masked output volume.
|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

<!== ===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.
-->

File:BRAINSROIAutoUI.png

2010-05-07T15:33:50Z

KentWilliams: uploaded a new version of "File:BRAINSROIAutoUI.png"

File:BRAINSROIAutoUI.png

2010-05-07T15:30:34Z

KentWilliams: uploaded a new version of "File:BRAINSROIAutoUI.png": Reverted to version as of 19:59, 6 May 2010

File:BRAINSROIAutoUI.png

2010-05-07T15:29:13Z

KentWilliams: uploaded a new version of "File:BRAINSROIAutoUI.png"

Documentation/3.6

2010-05-06T21:02:33Z

KentWilliams:

=Documentation Draft notes=
Key for flagged modules below:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module. If you're not sure how/where to add the link and module description:
* for command line modules, see other xml files (such as that for the GradientAnisotropicDiffusion Module) for an example of how to add documentation and links to wiki help.
* for interactive modules, see other modules in Base/GUI for an example.

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

=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 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 and the following [[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]]

=Main GUI=

*[[Image:WeakDoc.png]][[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)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=

==Core==
*[[Image:WeakDoc.png]][[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]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[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.
*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 theh 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:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (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|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

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

==Diffusion MRI==
*Diffusion MRI Welcome Module
* DWI filtering
**[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
**[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
**[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
* Diffusion tensor utilities
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
* Resampling
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
* Tractography
**[[Image:MissingOrStaleDocLink.png]][[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)

==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==
*[[Registration:Resampling|'''Overview of Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[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)
*[[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Image:MissingOrStaleDoc.png]][[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Scalar Volume Batch Make]] (Julien Finet)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*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
**[[Image:WeakDoc.png]][[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)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python 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)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[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)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

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

==Slicer Extensions==

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* 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 those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* 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) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@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) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[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-3.5|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'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

=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]]

'''Modules'''
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

'''Requirements for Modules'''
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

Modules:BRAINSResample

2010-05-06T21:01:49Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSResample

{|
|[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSResample is a program whose purpose is to resample image volumes to a new resolution, optionally applying a transformation.
== Usage ==
In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

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

{|
|

*Input Image Files
**Image To Warp: Input Image to transform/warp
**Reference Image: Defines the output space into which Image will be warped
**Deformation Field: Vector volume defining voxel transformation
*Warping Parameters
**Warp By Transform: Filename of BRAINSFit Transfrom file to use in place of deformation field
**Pixel Type: Specifies pixel type for input & output image. "binary" pixel type uses a modified algorithm whereby the image is read as unsigned char voxels, a signed distance map is created, te signed distance map is resampled, and the thresholded image is written to disk.
**Interpolation Mode: Specifies which interpolator is used.
**Invert Linear Transform: Perform transform inversion in ITK physical space before applying linear transform to the image.
*Result File
**Output Image: the input image, transformed/warped and then resampled into the reference image space.
|[[Image:BRAINSResampleUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

<!== ===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.
-->

Modules:BRAINSResample

2010-05-06T20:59:29Z

KentWilliams: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== BRAINSResample {| |[[Image:…'

File:BRAINSResampleUI.png

2010-05-06T20:32:50Z

KentWilliams:

Documentation/3.6

2010-05-06T20:19:49Z

KentWilliams:

=Documentation Draft notes=
Key for flagged modules below:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module. If you're not sure how/where to add the link and module description:
* for command line modules, see other xml files (such as that for the GradientAnisotropicDiffusion Module) for an example of how to add documentation and links to wiki help.
* for interactive modules, see other modules in Base/GUI for an example.

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

=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 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 and the following [[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]]

=Main GUI=

*[[Image:WeakDoc.png]][[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)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=

==Core==
*[[Image:WeakDoc.png]][[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]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[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.
*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).
** [[Image:MissingOrStaleDoc.png]][[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 theh 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:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (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|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

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

==Diffusion MRI==
*Diffusion MRI Welcome Module
* DWI filtering
**[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
**[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
**[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
* Diffusion tensor utilities
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
* Resampling
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
* Tractography
**[[Image:MissingOrStaleDocLink.png]][[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)

==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==
*[[Registration:Resampling|'''Overview of Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[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)
*[[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Image:MissingOrStaleDoc.png]][[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Scalar Volume Batch Make]] (Julien Finet)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*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
**[[Image:WeakDoc.png]][[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)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python 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)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[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)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

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

==Slicer Extensions==

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* 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 those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* 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) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@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) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[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-3.5|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'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

=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]]

'''Modules'''
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

'''Requirements for Modules'''
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

Modules:BRAINSROIAuto-Documentation-3.6

2010-05-06T20:18:55Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSROIAuto

{|
|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSROIAuto is a program whose purpose is to automatically generate a Binary Image (or Mask) to encompass the region in an brain image volume occupied by the brain.
== Usage ==
In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

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

{|
|
*IO Parameters
**Input Image Volume: Image for which mask should be generated
**Output Mask: Output binary image volume, defining the mask.
**Output Image Clipped by ROI: Optional image volume generated by masking the input image with the generated mask.
*Configuration Parameters
**Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.
**Otsu Threshold Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.
**Closing Size: The size for the largest void to fill in the mask, in voxels.
**Output Image Pixel Type: the scalar type of the masked output volume.
|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

<!== ===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.
-->

Modules:BRAINSROIAuto-Documentation-3.6

2010-05-06T20:17:55Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSROIAuto

{|
|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSROIAuto is a program whose purpose is to automatically generate a Binary Image (or Mask) to encompass the region in an brain image volume occupied by the brain.
== Usage ==
In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

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

{|
|
*IO Parameters
**Input Image Volume: Image for which mask should be generated
**Output Mask: Output binary image volume, defining the mask.
**Output Image Clipped by ROI: Optional image volume generated by masking the input image with the generated mask.
*Configuration Parameters
**Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.
**Otsu Threshold Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.
**Closing Size: The size for the largest void to fill in the mask, in voxels.
**Output Image Pixel Type: the scalar type of the masked output volume.
|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

<!== ===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.
-->

Modules:BRAINSROIAuto-Documentation-3.6

2010-05-06T20:16:52Z

KentWilliams: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== BRAINSROIAuto {| |[[Image:B…'

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSROIAuto

{|
|[[Image:BRAINSROIAutoUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSROIAuto is a program whose purpose is to automatically generate a Binary Image (or Mask) to encompass the region in an brain image volume occupied by the brain.
== Usage ==
In general, BRAINSROIAuto takes a brain image volume, and generates a mask without requiring parameter tweaking.

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
*IO Parameters
**Input Image Volume: Image for which mask should be generated
**Output Mask: Output binary image volume, defining the mask.
**Output Image Clipped by ROI: Optional image volume generated by masking the input image with the generated mask.
*Configuration Parameters
**Otsu Percentile Threshold: At what percentile should the Otsu Thresholding algorithm begin masking.
**Otsu Threshold Correction Factor: Used to scale the Otsu algorithm's results in cases where the mask generated is incorrect.
**Closing Size: The size for the largest void to fill in the mask, in voxels.
**Output Image Pixel Type: the scalar type of the masked output volume.
|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

File:BRAINSROIAutoUI.png

2010-05-06T19:59:56Z

KentWilliams:

Documentation/3.6

2010-05-06T19:57:27Z

KentWilliams:

=Documentation Draft notes=
Key for flagged modules below:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module. If you're not sure how/where to add the link and module description:
* for command line modules, see other xml files (such as that for the GradientAnisotropicDiffusion Module) for an example of how to add documentation and links to wiki help.
* for interactive modules, see other modules in Base/GUI for an example.

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

=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 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 and the following [[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]]

=Main GUI=

*[[Image:WeakDoc.png]][[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)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=

==Core==
*[[Image:WeakDoc.png]][[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]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[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.
*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).
** [[Image:MissingOrStaleDoc.png]][[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 theh 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:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (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|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

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

==Diffusion MRI==
*Diffusion MRI Welcome Module
* DWI filtering
**[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
**[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
**[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
* Diffusion tensor utilities
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
* Resampling
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
* Tractography
**[[Image:MissingOrStaleDocLink.png]][[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)

==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==
*[[Registration:Resampling|'''Overview of Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[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)
*[[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Image:MissingOrStaleDoc.png]][[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Scalar Volume Batch Make]] (Julien Finet)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*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
**[[Image:WeakDoc.png]][[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)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python 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)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[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)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

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

==Slicer Extensions==

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* 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 those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* 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) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@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) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[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-3.5|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'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

=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]]

'''Modules'''
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

'''Requirements for Modules'''
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

Modules:BRAINSFit

2010-05-06T19:56:28Z

KentWilliams:

Modules:BRAINSFit

2010-05-06T19:55:27Z

KentWilliams:

Modules:BRAINSFit

2010-05-06T19:40:10Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSFit

{|
|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSFit is a program for mutual information registration of brain imaging data using ITK classes. It is based on an example program included in the ITK distribution,

Insight/Examples/Registration/ImageRegistration8.cxx
This program is the most functional example of multi-modal 3D rigid image registration provided with ITK. ImageRegistration8 is in the Examples directory, and also sec. 8.5.3 in the ITK manual. We have modified and extended this example in several ways:

*defined a new ITK Transform class, based on itkScaleSkewVersor3DTransform which has 3 dimensions of scale but no skew aspect.
*implemented a set of functions to convert between Versor Transforms and the general itk::AffineTransform and deferred converting from specific to more general representations to preserve transform information specificity as long as possible. Our Rigid transform is the narrowest, a Versor rotation plus separate translation.
*Added a template class itkMultiModal3DMutualRegistrationHelper which is templated over the type of ITK transform generated, and the optimizer used.
*Added image masks as an optional input to the Registration algorithm, limiting the volume considered during registration to voxels within the brain.
*Added image mask generation as an optional input to the Registration algorithm when meaningful masks such as for whole brain are not available, allowing the fit to at least be focused on whole head tissue.
*Added the ability to use one transform result, such as the Rigid transform, to initialize a more adaptive transform
*Defined the command line parameters using tools from the Slicer [ 3] program, in order to conform to the Slicer3 Execution model.
Added the ability to write output images in any ITK-supported scalar image format.
*Through extensive testing as part of the BRAINS2 application suite, determined reasonable defaults for registration algorithm parameters.

== Usage ==
The BRAINSFit distribution contains a directory named TestData, which contains two example images. The first, test.nii.gz is a NIfTI format image volume, which is used the input for the CTest-managed regression test program. The program makexfrmedImage.cxx, included in the BRAINSFit distribution was used to generate test2.nii.gz, by scaling, rotating and translating test.nii.gz. You can see representative Sagittal slices of test.nii.gz (in this case, the fixed image, test2.nii.gz (the moving image), and the two images ’checkerboarded’ together to the right. To register test2.nii.gz to test.nii.gz, you can use the following command:

BRAINSFit --fixedVolume test.nii.gz \
--movingVolume test2.nii.gz \
--outputVolume registered.nii.gz \
--transformType Affine
A representative slice of the registered results image registered.nii.gz is to the right. You can see from the Checkerboard of the Fixed and Registered images that the fit is quite good with Affine transform-based registration. The blurring of the registered images is a consequence of the initial scaling used in generating the moving image from the fixed image, compounded by the interpolation necessitated by the transform operation.

You can see the differences in results if you re-run BRAINSFit using Rigid, ScaleVersor3D, or ScaleSkewVersor3D as the ----transformType parameter. In this case, the authors judged Affine the best method for registering these particular two images; in the BRAINS2 automated processing pipeline, Rigid usually works well for registering research scans.
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
*Required Input Parameters
**Fixed Image Volume: The fixed image for registration by mutual information optimization.
**MovingImage Volume: The moving image for registration by mutual information optimization.
**Transform Type: One of the four rigid ITK 3D transform types -- or BSpline -- to use in parameter optimization descent. BRAINSFit always optimizes mutual information, but the kind of descent varies with the transform type. The valid types are, Rigid, ScaleVersor3D, ScaleSkewVersor3D, Affine, and BSpline. Specifiying more than one in a comma separated list will initialize the next stage with the previous results. (default: Rigid)
*Transform Configuration Parameters
**Initialize Transform Mode: Determine how to initialize the transform center. GeometryOn on assumes that the center of the voxel lattice of the images represent similar structures. MomentsOn assumes that the center of mass of the images represent similar structures. CenterOfHead attempts to use the top of head and shape of neck to drive a center of mass estimate. Off assumes that the physical space of the images are close, and that centering in terms of the image Origins is a good starting point. This flag is mutually exclusive with the initialTransform flag. (default: Off)
** Infererior Cut Off From Center: the cut-off below the image centers, in millimeters, (default: 1000)
**Initial Tranform: Filename of transform used to initialize the registration.

--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)

-p, --promptUser
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer (default: 0)

-G, --gui
Display intermediate image volumes for debugging. NOTE: This is not
part of the standard build sytem, and probably does nothing on your
installation. (default: 0)

--projectedGradientTolerance <double>
From itkLBFGSBOptimizer.h: Set/Get the ProjectedGradientTolerance.
Algorithm terminates when the project gradient is below the tolerance.
Default lbfgsb value is 1e-5, but 1e-4 seems to work well. (default:
0.0001)

--costFunctionConvergenceFactor <double>
From itkLBFGSBOptimizer.h: Set/Get the CostFunctionConvergenceFactor.
Algorithm terminates when the reduction in cost function is less than
(factor * epsmcj) where epsmch is the machine precision. Typical
values for factor: 1e+12 for low accuracy; 1e+7 for moderate accuracy
and 1e+1 for extremely high accuracy. 1e+9 seems to work well.
(default: 1e+09)

--debugLevel <int>
Display debug messages, and produce debug intermediate results. 0=OFF
, 1=Minimal, 10=Maximum debugging. (default: 0)

--debugNumberOfThreads <int>
Explicitly specify the maximum number of threads to use. (default: -1)

--writeTransformOnFailure
Flag to save the final transform even if the numberOfIterations are
reached without convergence. (Intended for use when --failureExitCode
0 ) (default: 0)

--failureExitCode <int>
If the fit fails, exit with this status code. (It can be used to
force a successfult exit status of (0) if the registration fails due
to reaching the maximum number of iterations. (default: -1)

--maximumStepSize <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.2)

--relaxationFactor <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.5)

--useExplicitPDFDerivativesMode <AUTO|ON|OFF>
Using mode AUTO means OFF for BSplineDeformableTransforms and ON for
the linear transforms. The ON alternative uses more memory to
sometimes do a better job. (default: AUTO)

--useCachingOfBSplineWeightsMode <ON|OFF>
This is a 5x speed advantage at the expense of requiring much more
memory. Only relevant when transformType is BSpline. (default: ON)

--movingVolumeOrigin <std::vector<int>>
The coordinates of the origin of the moving image. This will
over-ride the information read from disk and is VERY DANGEROUS.
(default: 0,0,0)

--fixedVolumeOrigin <std::vector<int>>
The coordinates of the origin of the fixed image. This will over-ride
the information read from disk and is VERY DANGEROUS. (default: 0,0
,0)

--permitParameterVariation <std::vector<int>>
A bit vector to permit linear transform parameters to vary under
optimization. The vector order corresponds with transform parameters,
and beyond the end ones fill in as a default. For instance, you can
choose to rotate only in x (pitch) with 1,0,0; this is mostly for
expert use in turning on and off individual degrees of freedom in
rotation, translation or scaling without multiplying the number of
transform representations; this trick is probably meaningless when
tried with the general affine transform.

--studyID <std::string>
Identifier for the scanner encounter (MRQID), This will eventually be
removed. (default: ANON)

--patientID <std::string>
Identifier for the research subject, This will eventually be removed.
(default: ANON)

--numberOfMatchPoints <int>
the number of match points (default: 10)

--numberOfHistogramBins <int>
the number of histogram levels (default: 50)

-e, --histogramMatch
Histogram Match the input images. This is suitable for images of the
same modality that may have different absolute scales, but the same
overall intensity profile. (default: 0)

--medianFilterSize <std::vector<int>>
The radius for the optional MedianImageFilter preprocessing in all 3
directions. (default: 0,0,0)

--movingVolumeTimeIndex <int>
The index in the time series for the 3D moving image to fit, if
4-dimensional. (default: 0)

--fixedVolumeTimeIndex <int>
The index in the time series for the 3D fixed image to fit, if
4-dimensional. (default: 0)

--movingBinaryVolume <std::string>
Moving Image binary mask volume.

--fixedBinaryVolume <std::string>
Fixed Image binary mask volume.

--outputMovingVolumeROI <std::string>
The ROI automatically found in moving image.

--outputFixedVolumeROI <std::string>
The ROI automatically found in fixed image.

--maskProcessingMode <NOMASK|ROIAUTO|ROI>
What mode to use for using the masks. If ROIAUTO is choosen, then the
mask is implicitly defined using a otsu forground and hole filling
algorithm. The Region Of Interest mode (choose ROI) uses the masks to
define what parts of the image should be used for computing the
transform. (default: NOMASK)

--useWindowedSinc
Use windowedSinc interpolation to create output images. WARNING: This
will add 8 minutes to the interpolation of the final image of size
256x256x256. (default: 0)

--scaleOutputValues
If true, and the voxel values do not fit within the minimum and
maximum values of the desired outputVolumePixelType, then linearly
scale the min/max output image voxel values to fit within the min/max
range of the outputVolumePixelType. (default: 0)

--backgroundFillValue <double>
Background fill value for output image. (default: 0)

--outputVolumePixelType <float|short|ushort|int|uint|uchar>
The output image Pixel Type is the scalar datatype for representation
of the Output Volume. (default: float)

--outputVolume <std::string>
The (optional) output image for registration.

--strippedOutputTransform <std::string>
File name for the estimated transform, stripped of scaling, to
register the moving image to the fixed image.

--outputTransform <std::string>
Filename to which save the estimated transform.

--maxBSplineDisplacement <double>
Sets the maximum allowed displacements in image physical coordinates
for BSpline control grid along each axis. A value of 0.0 indicates
that the problem should be unbounded. NOTE: This only constrains the
BSpline portion, and does not limit the displacement from the
associated bulk transform. This can lead to a substantial reduction
in computation time in the BSpline optimizer. (default: 0)

--splineGridSize <std::vector<int>>
The number of subdivisions of the BSpline Grid to be centered on the
image space. Each dimension must have at least 3 subdivisions for the
BSpline to be correctly computed. (default: 14,10,12)

--skewScale <double>
ScaleSkewVersor3D Skew compensation factor. Increase this to put more
skew in a ScaleSkewVersor3D search pattern. 1.0 works well with a
translationScale of 1000.0 (default: 1)

--reproportionScale <double>
ScaleVersor3D 'Scale' compensation factor. Increase this to put more
rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern. 1.0
works well with a translationScale of 1000.0 (default: 1)

--translationScale <double>
How much to scale up changes in position compared to unit rotational
changes in radians -- decrease this to put more rotation in the search
pattern. (default: 1000)

--minimumStepSize <std::vector<double>>
Each step in the optimization takes steps at least this big. When
none are possible, registration is complete. (default: 0.005)

--numberOfSamples <int>
The number of voxels sampled for mutual information computation.
Increase this for a slower, more careful fit. You can also limit the
sampling focus with ROI masks and ROIAUTO mask generation. (default:
100000)

--numberOfIterations <std::vector<int>>
The maximum number of iterations to try before failing to converge.
Use an explicit limit like 500 or 1000 to manage risk of divergence
(default: 1500)

--initialTransform <std::string>

--initializeTransformMode <Off|MomentsOn|CenterOfHead|GeometryOn>
Determine how to initialize the transform center. GeometryOn on
assumes that the center of the voxel lattice of the images represent
similar structures. MomentsOn assumes that the center of mass of the
images represent similar structures. CenterOfHead attempts to use the
top of head and shape of neck to drive a center of mass estimate. Off
assumes that the physical space of the images are close, and that
centering in terms of the image Origins is a good starting point.
This flag is mutually exclusive with the initialTransform flag.
(default: Off)

|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:BRAINSFit

2010-05-06T19:35:21Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSFit

{|
|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSFit is a program for mutual information registration of brain imaging data using ITK classes. It is based on an example program included in the ITK distribution,

Insight/Examples/Registration/ImageRegistration8.cxx
This program is the most functional example of multi-modal 3D rigid image registration provided with ITK. ImageRegistration8 is in the Examples directory, and also sec. 8.5.3 in the ITK manual. We have modified and extended this example in several ways:

*defined a new ITK Transform class, based on itkScaleSkewVersor3DTransform which has 3 dimensions of scale but no skew aspect.
*implemented a set of functions to convert between Versor Transforms and the general itk::AffineTransform and deferred converting from specific to more general representations to preserve transform information specificity as long as possible. Our Rigid transform is the narrowest, a Versor rotation plus separate translation.
*Added a template class itkMultiModal3DMutualRegistrationHelper which is templated over the type of ITK transform generated, and the optimizer used.
*Added image masks as an optional input to the Registration algorithm, limiting the volume considered during registration to voxels within the brain.
*Added image mask generation as an optional input to the Registration algorithm when meaningful masks such as for whole brain are not available, allowing the fit to at least be focused on whole head tissue.
*Added the ability to use one transform result, such as the Rigid transform, to initialize a more adaptive transform
*Defined the command line parameters using tools from the Slicer [ 3] program, in order to conform to the Slicer3 Execution model.
Added the ability to write output images in any ITK-supported scalar image format.
*Through extensive testing as part of the BRAINS2 application suite, determined reasonable defaults for registration algorithm parameters.

== Usage ==
The BRAINSFit distribution contains a directory named TestData, which contains two example images. The first, test.nii.gz is a NIfTI format image volume, which is used the input for the CTest-managed regression test program. The program makexfrmedImage.cxx, included in the BRAINSFit distribution was used to generate test2.nii.gz, by scaling, rotating and translating test.nii.gz. You can see representative Sagittal slices of test.nii.gz (in this case, the fixed image, test2.nii.gz (the moving image), and the two images ’checkerboarded’ together to the right. To register test2.nii.gz to test.nii.gz, you can use the following command:

BRAINSFit --fixedVolume test.nii.gz \
--movingVolume test2.nii.gz \
--outputVolume registered.nii.gz \
--transformType Affine
A representative slice of the registered results image registered.nii.gz is to the right. You can see from the Checkerboard of the Fixed and Registered images that the fit is quite good with Affine transform-based registration. The blurring of the registered images is a consequence of the initial scaling used in generating the moving image from the fixed image, compounded by the interpolation necessitated by the transform operation.

You can see the differences in results if you re-run BRAINSFit using Rigid, ScaleVersor3D, or ScaleSkewVersor3D as the ----transformType parameter. In this case, the authors judged Affine the best method for registering these particular two images; in the BRAINS2 automated processing pipeline, Rigid usually works well for registering research scans.
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
*Fixed Image Volume: The fixed image for registration by mutual information optimization.
*MovingImage Volume: The moving image for registration by mutual information optimization.
*Transform Type: One of the four rigid ITK 3D transform types -- or BSpline -- to use in parameter optimization descent. BRAINSFit always optimizes mutual information, but the kind of descent varies with the transform type. The valid types are, Rigid, ScaleVersor3D, ScaleSkewVersor3D, Affine, and BSpline. Specifiying more than one in a comma separated list will initialize the next stage with the previous results. (default: Rigid)

--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)

-p, --promptUser
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer (default: 0)

-G, --gui
Display intermediate image volumes for debugging. NOTE: This is not
part of the standard build sytem, and probably does nothing on your
installation. (default: 0)

--projectedGradientTolerance <double>
From itkLBFGSBOptimizer.h: Set/Get the ProjectedGradientTolerance.
Algorithm terminates when the project gradient is below the tolerance.
Default lbfgsb value is 1e-5, but 1e-4 seems to work well. (default:
0.0001)

--costFunctionConvergenceFactor <double>
From itkLBFGSBOptimizer.h: Set/Get the CostFunctionConvergenceFactor.
Algorithm terminates when the reduction in cost function is less than
(factor * epsmcj) where epsmch is the machine precision. Typical
values for factor: 1e+12 for low accuracy; 1e+7 for moderate accuracy
and 1e+1 for extremely high accuracy. 1e+9 seems to work well.
(default: 1e+09)

--debugLevel <int>
Display debug messages, and produce debug intermediate results. 0=OFF
, 1=Minimal, 10=Maximum debugging. (default: 0)

--debugNumberOfThreads <int>
Explicitly specify the maximum number of threads to use. (default: -1)

--writeTransformOnFailure
Flag to save the final transform even if the numberOfIterations are
reached without convergence. (Intended for use when --failureExitCode
0 ) (default: 0)

--failureExitCode <int>
If the fit fails, exit with this status code. (It can be used to
force a successfult exit status of (0) if the registration fails due
to reaching the maximum number of iterations. (default: -1)

--maximumStepSize <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.2)

--relaxationFactor <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.5)

--useExplicitPDFDerivativesMode <AUTO|ON|OFF>
Using mode AUTO means OFF for BSplineDeformableTransforms and ON for
the linear transforms. The ON alternative uses more memory to
sometimes do a better job. (default: AUTO)

--useCachingOfBSplineWeightsMode <ON|OFF>
This is a 5x speed advantage at the expense of requiring much more
memory. Only relevant when transformType is BSpline. (default: ON)

--movingVolumeOrigin <std::vector<int>>
The coordinates of the origin of the moving image. This will
over-ride the information read from disk and is VERY DANGEROUS.
(default: 0,0,0)

--fixedVolumeOrigin <std::vector<int>>
The coordinates of the origin of the fixed image. This will over-ride
the information read from disk and is VERY DANGEROUS. (default: 0,0
,0)

--permitParameterVariation <std::vector<int>>
A bit vector to permit linear transform parameters to vary under
optimization. The vector order corresponds with transform parameters,
and beyond the end ones fill in as a default. For instance, you can
choose to rotate only in x (pitch) with 1,0,0; this is mostly for
expert use in turning on and off individual degrees of freedom in
rotation, translation or scaling without multiplying the number of
transform representations; this trick is probably meaningless when
tried with the general affine transform.

--studyID <std::string>
Identifier for the scanner encounter (MRQID), This will eventually be
removed. (default: ANON)

--patientID <std::string>
Identifier for the research subject, This will eventually be removed.
(default: ANON)

--numberOfMatchPoints <int>
the number of match points (default: 10)

--numberOfHistogramBins <int>
the number of histogram levels (default: 50)

-e, --histogramMatch
Histogram Match the input images. This is suitable for images of the
same modality that may have different absolute scales, but the same
overall intensity profile. (default: 0)

--medianFilterSize <std::vector<int>>
The radius for the optional MedianImageFilter preprocessing in all 3
directions. (default: 0,0,0)

--movingVolumeTimeIndex <int>
The index in the time series for the 3D moving image to fit, if
4-dimensional. (default: 0)

--fixedVolumeTimeIndex <int>
The index in the time series for the 3D fixed image to fit, if
4-dimensional. (default: 0)

--movingBinaryVolume <std::string>
Moving Image binary mask volume.

--fixedBinaryVolume <std::string>
Fixed Image binary mask volume.

--outputMovingVolumeROI <std::string>
The ROI automatically found in moving image.

--outputFixedVolumeROI <std::string>
The ROI automatically found in fixed image.

--maskProcessingMode <NOMASK|ROIAUTO|ROI>
What mode to use for using the masks. If ROIAUTO is choosen, then the
mask is implicitly defined using a otsu forground and hole filling
algorithm. The Region Of Interest mode (choose ROI) uses the masks to
define what parts of the image should be used for computing the
transform. (default: NOMASK)

--useWindowedSinc
Use windowedSinc interpolation to create output images. WARNING: This
will add 8 minutes to the interpolation of the final image of size
256x256x256. (default: 0)

--scaleOutputValues
If true, and the voxel values do not fit within the minimum and
maximum values of the desired outputVolumePixelType, then linearly
scale the min/max output image voxel values to fit within the min/max
range of the outputVolumePixelType. (default: 0)

--backgroundFillValue <double>
Background fill value for output image. (default: 0)

--outputVolumePixelType <float|short|ushort|int|uint|uchar>
The output image Pixel Type is the scalar datatype for representation
of the Output Volume. (default: float)

--outputVolume <std::string>
The (optional) output image for registration.

--strippedOutputTransform <std::string>
File name for the estimated transform, stripped of scaling, to
register the moving image to the fixed image.

--outputTransform <std::string>
Filename to which save the estimated transform.

--maxBSplineDisplacement <double>
Sets the maximum allowed displacements in image physical coordinates
for BSpline control grid along each axis. A value of 0.0 indicates
that the problem should be unbounded. NOTE: This only constrains the
BSpline portion, and does not limit the displacement from the
associated bulk transform. This can lead to a substantial reduction
in computation time in the BSpline optimizer. (default: 0)

--splineGridSize <std::vector<int>>
The number of subdivisions of the BSpline Grid to be centered on the
image space. Each dimension must have at least 3 subdivisions for the
BSpline to be correctly computed. (default: 14,10,12)

--skewScale <double>
ScaleSkewVersor3D Skew compensation factor. Increase this to put more
skew in a ScaleSkewVersor3D search pattern. 1.0 works well with a
translationScale of 1000.0 (default: 1)

--reproportionScale <double>
ScaleVersor3D 'Scale' compensation factor. Increase this to put more
rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern. 1.0
works well with a translationScale of 1000.0 (default: 1)

--translationScale <double>
How much to scale up changes in position compared to unit rotational
changes in radians -- decrease this to put more rotation in the search
pattern. (default: 1000)

--minimumStepSize <std::vector<double>>
Each step in the optimization takes steps at least this big. When
none are possible, registration is complete. (default: 0.005)

--numberOfSamples <int>
The number of voxels sampled for mutual information computation.
Increase this for a slower, more careful fit. You can also limit the
sampling focus with ROI masks and ROIAUTO mask generation. (default:
100000)

--numberOfIterations <std::vector<int>>
The maximum number of iterations to try before failing to converge.
Use an explicit limit like 500 or 1000 to manage risk of divergence
(default: 1500)

--initialTransform <std::string>
Filename of transform used to initialize the registration.

--maskInferiorCutOffFromCenter <double>
For use with --initializeTransformMode CenterOfHead (and
--maskProcessingMode ROIAUTO): the cut-off below the image centers, in
millimeters, (default: 1000)

--initializeTransformMode <Off|MomentsOn|CenterOfHead|GeometryOn>
Determine how to initialize the transform center. GeometryOn on
assumes that the center of the voxel lattice of the images represent
similar structures. MomentsOn assumes that the center of mass of the
images represent similar structures. CenterOfHead attempts to use the
top of head and shape of neck to drive a center of mass estimate. Off
assumes that the physical space of the images are close, and that
centering in terms of the image Origins is a good starting point.
This flag is mutually exclusive with the initialTransform flag.
(default: Off)

|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:BRAINSFit

2010-05-06T19:33:52Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSFit

{|
|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSFit is a program for mutual information registration of brain imaging data using ITK classes. It is based on an example program included in the ITK distribution,

Insight/Examples/Registration/ImageRegistration8.cxx
This program is the most functional example of multi-modal 3D rigid image registration provided with ITK. ImageRegistration8 is in the Examples directory, and also sec. 8.5.3 in the ITK manual. We have modified and extended this example in several ways:

*defined a new ITK Transform class, based on itkScaleSkewVersor3DTransform which has 3 dimensions of scale but no skew aspect.
*implemented a set of functions to convert between Versor Transforms and the general itk::AffineTransform and deferred converting from specific to more general representations to preserve transform information specificity as long as possible. Our Rigid transform is the narrowest, a Versor rotation plus separate translation.
*Added a template class itkMultiModal3DMutualRegistrationHelper which is templated over the type of ITK transform generated, and the optimizer used.
*Added image masks as an optional input to the Registration algorithm, limiting the volume considered during registration to voxels within the brain.
*Added image mask generation as an optional input to the Registration algorithm when meaningful masks such as for whole brain are not available, allowing the fit to at least be focused on whole head tissue.
*Added the ability to use one transform result, such as the Rigid transform, to initialize a more adaptive transform
*Defined the command line parameters using tools from the Slicer [ 3] program, in order to conform to the Slicer3 Execution model.
Added the ability to write output images in any ITK-supported scalar image format.
*Through extensive testing as part of the BRAINS2 application suite, determined reasonable defaults for registration algorithm parameters.

== Usage ==
The BRAINSFit distribution contains a directory named TestData, which contains two example images. The first, test.nii.gz is a NIfTI format image volume, which is used the input for the CTest-managed regression test program. The program makexfrmedImage.cxx, included in the BRAINSFit distribution was used to generate test2.nii.gz, by scaling, rotating and translating test.nii.gz. You can see representative Sagittal slices of test.nii.gz (in this case, the fixed image, test2.nii.gz (the moving image), and the two images ’checkerboarded’ together to the right. To register test2.nii.gz to test.nii.gz, you can use the following command:

BRAINSFit --fixedVolume test.nii.gz \
--movingVolume test2.nii.gz \
--outputVolume registered.nii.gz \
--transformType Affine
A representative slice of the registered results image registered.nii.gz is to the right. You can see from the Checkerboard of the Fixed and Registered images that the fit is quite good with Affine transform-based registration. The blurring of the registered images is a consequence of the initial scaling used in generating the moving image from the fixed image, compounded by the interpolation necessitated by the transform operation.

You can see the differences in results if you re-run BRAINSFit using Rigid, ScaleVersor3D, or ScaleSkewVersor3D as the ----transformType parameter. In this case, the authors judged Affine the best method for registering these particular two images; in the BRAINS2 automated processing pipeline, Rigid usually works well for registering research scans.
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|

Fixed Image Volume: The fixed image for registration by mutual information optimization.
MovingImage Volume: The moving image for registration by mutual information optimization.
Transform Type: One of the four rigid ITK 3D transform types -- or BSpline -- to use in parameter optimization descent. BRAINSFit always optimizes mutual information, but the kind of descent varies with the transform type. The valid types are, Rigid, ScaleVersor3D, ScaleSkewVersor3D, Affine, and BSpline. Specifiying more than one in a comma separated list will initialize the next stage with the previous results. (default: Rigid)

--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)

-p, --promptUser
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer (default: 0)

-G, --gui
Display intermediate image volumes for debugging. NOTE: This is not
part of the standard build sytem, and probably does nothing on your
installation. (default: 0)

--projectedGradientTolerance <double>
From itkLBFGSBOptimizer.h: Set/Get the ProjectedGradientTolerance.
Algorithm terminates when the project gradient is below the tolerance.
Default lbfgsb value is 1e-5, but 1e-4 seems to work well. (default:
0.0001)

--costFunctionConvergenceFactor <double>
From itkLBFGSBOptimizer.h: Set/Get the CostFunctionConvergenceFactor.
Algorithm terminates when the reduction in cost function is less than
(factor * epsmcj) where epsmch is the machine precision. Typical
values for factor: 1e+12 for low accuracy; 1e+7 for moderate accuracy
and 1e+1 for extremely high accuracy. 1e+9 seems to work well.
(default: 1e+09)

--debugLevel <int>
Display debug messages, and produce debug intermediate results. 0=OFF
, 1=Minimal, 10=Maximum debugging. (default: 0)

--debugNumberOfThreads <int>
Explicitly specify the maximum number of threads to use. (default: -1)

--writeTransformOnFailure
Flag to save the final transform even if the numberOfIterations are
reached without convergence. (Intended for use when --failureExitCode
0 ) (default: 0)

--failureExitCode <int>
If the fit fails, exit with this status code. (It can be used to
force a successfult exit status of (0) if the registration fails due
to reaching the maximum number of iterations. (default: -1)

--maximumStepSize <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.2)

--relaxationFactor <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.5)

--useExplicitPDFDerivativesMode <AUTO|ON|OFF>
Using mode AUTO means OFF for BSplineDeformableTransforms and ON for
the linear transforms. The ON alternative uses more memory to
sometimes do a better job. (default: AUTO)

--useCachingOfBSplineWeightsMode <ON|OFF>
This is a 5x speed advantage at the expense of requiring much more
memory. Only relevant when transformType is BSpline. (default: ON)

--movingVolumeOrigin <std::vector<int>>
The coordinates of the origin of the moving image. This will
over-ride the information read from disk and is VERY DANGEROUS.
(default: 0,0,0)

--fixedVolumeOrigin <std::vector<int>>
The coordinates of the origin of the fixed image. This will over-ride
the information read from disk and is VERY DANGEROUS. (default: 0,0
,0)

--permitParameterVariation <std::vector<int>>
A bit vector to permit linear transform parameters to vary under
optimization. The vector order corresponds with transform parameters,
and beyond the end ones fill in as a default. For instance, you can
choose to rotate only in x (pitch) with 1,0,0; this is mostly for
expert use in turning on and off individual degrees of freedom in
rotation, translation or scaling without multiplying the number of
transform representations; this trick is probably meaningless when
tried with the general affine transform.

--studyID <std::string>
Identifier for the scanner encounter (MRQID), This will eventually be
removed. (default: ANON)

--patientID <std::string>
Identifier for the research subject, This will eventually be removed.
(default: ANON)

--numberOfMatchPoints <int>
the number of match points (default: 10)

--numberOfHistogramBins <int>
the number of histogram levels (default: 50)

-e, --histogramMatch
Histogram Match the input images. This is suitable for images of the
same modality that may have different absolute scales, but the same
overall intensity profile. (default: 0)

--medianFilterSize <std::vector<int>>
The radius for the optional MedianImageFilter preprocessing in all 3
directions. (default: 0,0,0)

--movingVolumeTimeIndex <int>
The index in the time series for the 3D moving image to fit, if
4-dimensional. (default: 0)

--fixedVolumeTimeIndex <int>
The index in the time series for the 3D fixed image to fit, if
4-dimensional. (default: 0)

--movingBinaryVolume <std::string>
Moving Image binary mask volume.

--fixedBinaryVolume <std::string>
Fixed Image binary mask volume.

--outputMovingVolumeROI <std::string>
The ROI automatically found in moving image.

--outputFixedVolumeROI <std::string>
The ROI automatically found in fixed image.

--maskProcessingMode <NOMASK|ROIAUTO|ROI>
What mode to use for using the masks. If ROIAUTO is choosen, then the
mask is implicitly defined using a otsu forground and hole filling
algorithm. The Region Of Interest mode (choose ROI) uses the masks to
define what parts of the image should be used for computing the
transform. (default: NOMASK)

--useWindowedSinc
Use windowedSinc interpolation to create output images. WARNING: This
will add 8 minutes to the interpolation of the final image of size
256x256x256. (default: 0)

--scaleOutputValues
If true, and the voxel values do not fit within the minimum and
maximum values of the desired outputVolumePixelType, then linearly
scale the min/max output image voxel values to fit within the min/max
range of the outputVolumePixelType. (default: 0)

--backgroundFillValue <double>
Background fill value for output image. (default: 0)

--outputVolumePixelType <float|short|ushort|int|uint|uchar>
The output image Pixel Type is the scalar datatype for representation
of the Output Volume. (default: float)

--outputVolume <std::string>
The (optional) output image for registration.

--strippedOutputTransform <std::string>
File name for the estimated transform, stripped of scaling, to
register the moving image to the fixed image.

--outputTransform <std::string>
Filename to which save the estimated transform.

--maxBSplineDisplacement <double>
Sets the maximum allowed displacements in image physical coordinates
for BSpline control grid along each axis. A value of 0.0 indicates
that the problem should be unbounded. NOTE: This only constrains the
BSpline portion, and does not limit the displacement from the
associated bulk transform. This can lead to a substantial reduction
in computation time in the BSpline optimizer. (default: 0)

--splineGridSize <std::vector<int>>
The number of subdivisions of the BSpline Grid to be centered on the
image space. Each dimension must have at least 3 subdivisions for the
BSpline to be correctly computed. (default: 14,10,12)

--skewScale <double>
ScaleSkewVersor3D Skew compensation factor. Increase this to put more
skew in a ScaleSkewVersor3D search pattern. 1.0 works well with a
translationScale of 1000.0 (default: 1)

--reproportionScale <double>
ScaleVersor3D 'Scale' compensation factor. Increase this to put more
rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern. 1.0
works well with a translationScale of 1000.0 (default: 1)

--translationScale <double>
How much to scale up changes in position compared to unit rotational
changes in radians -- decrease this to put more rotation in the search
pattern. (default: 1000)

--minimumStepSize <std::vector<double>>
Each step in the optimization takes steps at least this big. When
none are possible, registration is complete. (default: 0.005)

--numberOfSamples <int>
The number of voxels sampled for mutual information computation.
Increase this for a slower, more careful fit. You can also limit the
sampling focus with ROI masks and ROIAUTO mask generation. (default:
100000)

--numberOfIterations <std::vector<int>>
The maximum number of iterations to try before failing to converge.
Use an explicit limit like 500 or 1000 to manage risk of divergence
(default: 1500)

--initialTransform <std::string>
Filename of transform used to initialize the registration.

--maskInferiorCutOffFromCenter <double>
For use with --initializeTransformMode CenterOfHead (and
--maskProcessingMode ROIAUTO): the cut-off below the image centers, in
millimeters, (default: 1000)

--initializeTransformMode <Off|MomentsOn|CenterOfHead|GeometryOn>
Determine how to initialize the transform center. GeometryOn on
assumes that the center of the voxel lattice of the images represent
similar structures. MomentsOn assumes that the center of mass of the
images represent similar structures. CenterOfHead attempts to use the
top of head and shape of neck to drive a center of mass estimate. Off
assumes that the physical space of the images are close, and that
centering in terms of the image Origins is a good starting point.
This flag is mutually exclusive with the initialTransform flag.
(default: Off)

|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:BRAINSFit

2010-05-06T19:29:57Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSFit

{|
|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSFit is a program for mutual information registration of brain imaging data using ITK classes. It is based on an example program included in the ITK distribution,

Insight/Examples/Registration/ImageRegistration8.cxx
This program is the most functional example of multi-modal 3D rigid image registration provided with ITK. ImageRegistration8 is in the Examples directory, and also sec. 8.5.3 in the ITK manual. We have modified and extended this example in several ways:

*defined a new ITK Transform class, based on itkScaleSkewVersor3DTransform which has 3 dimensions of scale but no skew aspect.
*implemented a set of functions to convert between Versor Transforms and the general itk::AffineTransform and deferred converting from specific to more general representations to preserve transform information specificity as long as possible. Our Rigid transform is the narrowest, a Versor rotation plus separate translation.
*Added a template class itkMultiModal3DMutualRegistrationHelper which is templated over the type of ITK transform generated, and the optimizer used.
*Added image masks as an optional input to the Registration algorithm, limiting the volume considered during registration to voxels within the brain.
*Added image mask generation as an optional input to the Registration algorithm when meaningful masks such as for whole brain are not available, allowing the fit to at least be focused on whole head tissue.
*Added the ability to use one transform result, such as the Rigid transform, to initialize a more adaptive transform
*Defined the command line parameters using tools from the Slicer [ 3] program, in order to conform to the Slicer3 Execution model.
Added the ability to write output images in any ITK-supported scalar image format.
*Through extensive testing as part of the BRAINS2 application suite, determined reasonable defaults for registration algorithm parameters.

== Usage ==
The BRAINSFit distribution contains a directory named TestData, which contains two example images. The first, test.nii.gz is a NIfTI format image volume, which is used the input for the CTest-managed regression test program. The program makexfrmedImage.cxx, included in the BRAINSFit distribution was used to generate test2.nii.gz, by scaling, rotating and translating test.nii.gz. You can see representative Sagittal slices of test.nii.gz (in this case, the fixed image, test2.nii.gz (the moving image), and the two images ’checkerboarded’ together to the right. To register test2.nii.gz to test.nii.gz, you can use the following command:

BRAINSFit --fixedVolume test.nii.gz \
--movingVolume test2.nii.gz \
--outputVolume registered.nii.gz \
--transformType Affine
A representative slice of the registered results image registered.nii.gz is to the right. You can see from the Checkerboard of the Fixed and Registered images that the fit is quite good with Affine transform-based registration. The blurring of the registered images is a consequence of the initial scaling used in generating the moving image from the fixed image, compounded by the interpolation necessitated by the transform operation.

You can see the differences in results if you re-run BRAINSFit using Rigid, ScaleVersor3D, or ScaleSkewVersor3D as the ----transformType parameter. In this case, the authors judged Affine the best method for registering these particular two images; in the BRAINS2 automated processing pipeline, Rigid usually works well for registering research scans.
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|

--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)

-p, --promptUser
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer (default: 0)

-G, --gui
Display intermediate image volumes for debugging. NOTE: This is not
part of the standard build sytem, and probably does nothing on your
installation. (default: 0)

--projectedGradientTolerance <double>
From itkLBFGSBOptimizer.h: Set/Get the ProjectedGradientTolerance.
Algorithm terminates when the project gradient is below the tolerance.
Default lbfgsb value is 1e-5, but 1e-4 seems to work well. (default:
0.0001)

--costFunctionConvergenceFactor <double>
From itkLBFGSBOptimizer.h: Set/Get the CostFunctionConvergenceFactor.
Algorithm terminates when the reduction in cost function is less than
(factor * epsmcj) where epsmch is the machine precision. Typical
values for factor: 1e+12 for low accuracy; 1e+7 for moderate accuracy
and 1e+1 for extremely high accuracy. 1e+9 seems to work well.
(default: 1e+09)

--debugLevel <int>
Display debug messages, and produce debug intermediate results. 0=OFF
, 1=Minimal, 10=Maximum debugging. (default: 0)

--debugNumberOfThreads <int>
Explicitly specify the maximum number of threads to use. (default: -1)

--writeTransformOnFailure
Flag to save the final transform even if the numberOfIterations are
reached without convergence. (Intended for use when --failureExitCode
0 ) (default: 0)

--failureExitCode <int>
If the fit fails, exit with this status code. (It can be used to
force a successfult exit status of (0) if the registration fails due
to reaching the maximum number of iterations. (default: -1)

--maximumStepSize <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.2)

--relaxationFactor <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.5)

--useExplicitPDFDerivativesMode <AUTO|ON|OFF>
Using mode AUTO means OFF for BSplineDeformableTransforms and ON for
the linear transforms. The ON alternative uses more memory to
sometimes do a better job. (default: AUTO)

--useCachingOfBSplineWeightsMode <ON|OFF>
This is a 5x speed advantage at the expense of requiring much more
memory. Only relevant when transformType is BSpline. (default: ON)

--movingVolumeOrigin <std::vector<int>>
The coordinates of the origin of the moving image. This will
over-ride the information read from disk and is VERY DANGEROUS.
(default: 0,0,0)

--fixedVolumeOrigin <std::vector<int>>
The coordinates of the origin of the fixed image. This will over-ride
the information read from disk and is VERY DANGEROUS. (default: 0,0
,0)

--permitParameterVariation <std::vector<int>>
A bit vector to permit linear transform parameters to vary under
optimization. The vector order corresponds with transform parameters,
and beyond the end ones fill in as a default. For instance, you can
choose to rotate only in x (pitch) with 1,0,0; this is mostly for
expert use in turning on and off individual degrees of freedom in
rotation, translation or scaling without multiplying the number of
transform representations; this trick is probably meaningless when
tried with the general affine transform.

--studyID <std::string>
Identifier for the scanner encounter (MRQID), This will eventually be
removed. (default: ANON)

--patientID <std::string>
Identifier for the research subject, This will eventually be removed.
(default: ANON)

--numberOfMatchPoints <int>
the number of match points (default: 10)

--numberOfHistogramBins <int>
the number of histogram levels (default: 50)

-e, --histogramMatch
Histogram Match the input images. This is suitable for images of the
same modality that may have different absolute scales, but the same
overall intensity profile. (default: 0)

--medianFilterSize <std::vector<int>>
The radius for the optional MedianImageFilter preprocessing in all 3
directions. (default: 0,0,0)

--movingVolumeTimeIndex <int>
The index in the time series for the 3D moving image to fit, if
4-dimensional. (default: 0)

--fixedVolumeTimeIndex <int>
The index in the time series for the 3D fixed image to fit, if
4-dimensional. (default: 0)

--movingBinaryVolume <std::string>
Moving Image binary mask volume.

--fixedBinaryVolume <std::string>
Fixed Image binary mask volume.

--outputMovingVolumeROI <std::string>
The ROI automatically found in moving image.

--outputFixedVolumeROI <std::string>
The ROI automatically found in fixed image.

--maskProcessingMode <NOMASK|ROIAUTO|ROI>
What mode to use for using the masks. If ROIAUTO is choosen, then the
mask is implicitly defined using a otsu forground and hole filling
algorithm. The Region Of Interest mode (choose ROI) uses the masks to
define what parts of the image should be used for computing the
transform. (default: NOMASK)

--useWindowedSinc
Use windowedSinc interpolation to create output images. WARNING: This
will add 8 minutes to the interpolation of the final image of size
256x256x256. (default: 0)

--scaleOutputValues
If true, and the voxel values do not fit within the minimum and
maximum values of the desired outputVolumePixelType, then linearly
scale the min/max output image voxel values to fit within the min/max
range of the outputVolumePixelType. (default: 0)

--backgroundFillValue <double>
Background fill value for output image. (default: 0)

--outputVolumePixelType <float|short|ushort|int|uint|uchar>
The output image Pixel Type is the scalar datatype for representation
of the Output Volume. (default: float)

--outputVolume <std::string>
The (optional) output image for registration.

--strippedOutputTransform <std::string>
File name for the estimated transform, stripped of scaling, to
register the moving image to the fixed image.

--outputTransform <std::string>
Filename to which save the estimated transform.

--maxBSplineDisplacement <double>
Sets the maximum allowed displacements in image physical coordinates
for BSpline control grid along each axis. A value of 0.0 indicates
that the problem should be unbounded. NOTE: This only constrains the
BSpline portion, and does not limit the displacement from the
associated bulk transform. This can lead to a substantial reduction
in computation time in the BSpline optimizer. (default: 0)

--splineGridSize <std::vector<int>>
The number of subdivisions of the BSpline Grid to be centered on the
image space. Each dimension must have at least 3 subdivisions for the
BSpline to be correctly computed. (default: 14,10,12)

--skewScale <double>
ScaleSkewVersor3D Skew compensation factor. Increase this to put more
skew in a ScaleSkewVersor3D search pattern. 1.0 works well with a
translationScale of 1000.0 (default: 1)

--reproportionScale <double>
ScaleVersor3D 'Scale' compensation factor. Increase this to put more
rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern. 1.0
works well with a translationScale of 1000.0 (default: 1)

--translationScale <double>
How much to scale up changes in position compared to unit rotational
changes in radians -- decrease this to put more rotation in the search
pattern. (default: 1000)

--minimumStepSize <std::vector<double>>
Each step in the optimization takes steps at least this big. When
none are possible, registration is complete. (default: 0.005)

--numberOfSamples <int>
The number of voxels sampled for mutual information computation.
Increase this for a slower, more careful fit. You can also limit the
sampling focus with ROI masks and ROIAUTO mask generation. (default:
100000)

--numberOfIterations <std::vector<int>>
The maximum number of iterations to try before failing to converge.
Use an explicit limit like 500 or 1000 to manage risk of divergence
(default: 1500)

--initialTransform <std::string>
Filename of transform used to initialize the registration.

--maskInferiorCutOffFromCenter <double>
For use with --initializeTransformMode CenterOfHead (and
--maskProcessingMode ROIAUTO): the cut-off below the image centers, in
millimeters, (default: 1000)

--initializeTransformMode <Off|MomentsOn|CenterOfHead|GeometryOn>
Determine how to initialize the transform center. GeometryOn on
assumes that the center of the voxel lattice of the images represent
similar structures. MomentsOn assumes that the center of mass of the
images represent similar structures. CenterOfHead attempts to use the
top of head and shape of neck to drive a center of mass estimate. Off
assumes that the physical space of the images are close, and that
centering in terms of the image Origins is a good starting point.
This flag is mutually exclusive with the initialTransform flag.
(default: Off)

--transformType <std::vector<std::string>>
Specifies one of the four rigid ITK 3D transform types -- or BSpline
-- to use in parameter optimization descent. BRAINSFit always
optimizes mutual information, but the kind of descent varies with the
transform type. The valid types are, Rigid, ScaleVersor3D,
ScaleSkewVersor3D, Affine, and BSpline. Specifiying more than one in
a comma separated list will initialize the next stage with the
previous results. (default: Rigid)

--movingVolume <std::string>
The moving image for registration by mutual information optimization.

--fixedVolume <std::string>
The fixed image for registration by mutual information optimization.

|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:BRAINSFit

2010-05-06T19:29:04Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
BRAINSFit

{|
|[[Image:BRAINSFitUI.png|thumb|280px|User Interface]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Author1: Hans Johnson, University of Iowa
* Contributor1: Kent WIlliams, University of Iowa
* Contact: Hans Johnson, hans-johson at uiowa.edu

===Module Description===
BRAINSFit is a program for mutual information registration of brain imaging data using ITK classes. It is based on an example program included in the ITK distribution,

Insight/Examples/Registration/ImageRegistration8.cxx
This program is the most functional example of multi-modal 3D rigid image registration provided with ITK. ImageRegistration8 is in the Examples directory, and also sec. 8.5.3 in the ITK manual. We have modified and extended this example in several ways:

*defined a new ITK Transform class, based on itkScaleSkewVersor3DTransform which has 3 dimensions of scale but no skew aspect.
*implemented a set of functions to convert between Versor Transforms and the general itk::AffineTransform and deferred converting from specific to more general representations to preserve transform information specificity as long as possible. Our Rigid transform is the narrowest, a Versor rotation plus separate translation.
*Added a template class itkMultiModal3DMutualRegistrationHelper which is templated over the type of ITK transform generated, and the optimizer used.
*Added image masks as an optional input to the Registration algorithm, limiting the volume considered during registration to voxels within the brain.
*Added image mask generation as an optional input to the Registration algorithm when meaningful masks such as for whole brain are not available, allowing the fit to at least be focused on whole head tissue.
*Added the ability to use one transform result, such as the Rigid transform, to initialize a more adaptive transform
*Defined the command line parameters using tools from the Slicer [ 3] program, in order to conform to the Slicer3 Execution model.
Added the ability to write output images in any ITK-supported scalar image format.
*Through extensive testing as part of the BRAINS2 application suite, determined reasonable defaults for registration algorithm parameters.

== Usage ==
The BRAINSFit distribution contains a directory named TestData, which contains two example images. The first, test.nii.gz is a NIfTI format image volume, which is used the input for the CTest-managed regression test program. The program makexfrmedImage.cxx, included in the BRAINSFit distribution was used to generate test2.nii.gz, by scaling, rotating and translating test.nii.gz. You can see representative Sagittal slices of test.nii.gz (in this case, the fixed image, test2.nii.gz (the moving image), and the two images ’checkerboarded’ together to the right. To register test2.nii.gz to test.nii.gz, you can use the following command:

BRAINSFit --fixedVolume test.nii.gz \
--movingVolume test2.nii.gz \
--outputVolume registered.nii.gz \
--transformType Affine
A representative slice of the registered results image registered.nii.gz is to the right. You can see from the Checkerboard of the Fixed and Registered images that the fit is quite good with Affine transform-based registration. The blurring of the registered images is a consequence of the initial scaling used in generating the moving image from the fixed image, compounded by the interpolation necessitated by the transform operation.

You can see the differences in results if you re-run BRAINSFit using Rigid, ScaleVersor3D, or ScaleSkewVersor3D as the ----transformType parameter. In this case, the authors judged Affine the best method for registering these particular two images; in the BRAINS2 automated processing pipeline, Rigid usually works well for registering research scans.
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|

--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)

-p, --promptUser
Prompt the user to hit enter each time an image is sent to the
DebugImageViewer (default: 0)

-G, --gui
Display intermediate image volumes for debugging. NOTE: This is not
part of the standard build sytem, and probably does nothing on your
installation. (default: 0)

--projectedGradientTolerance <double>
From itkLBFGSBOptimizer.h: Set/Get the ProjectedGradientTolerance.
Algorithm terminates when the project gradient is below the tolerance.
Default lbfgsb value is 1e-5, but 1e-4 seems to work well. (default:
0.0001)

--costFunctionConvergenceFactor <double>
From itkLBFGSBOptimizer.h: Set/Get the CostFunctionConvergenceFactor.
Algorithm terminates when the reduction in cost function is less than
(factor * epsmcj) where epsmch is the machine precision. Typical
values for factor: 1e+12 for low accuracy; 1e+7 for moderate accuracy
and 1e+1 for extremely high accuracy. 1e+9 seems to work well.
(default: 1e+09)

--debugLevel <int>
Display debug messages, and produce debug intermediate results. 0=OFF
, 1=Minimal, 10=Maximum debugging. (default: 0)

--debugNumberOfThreads <int>
Explicitly specify the maximum number of threads to use. (default: -1)

--writeTransformOnFailure
Flag to save the final transform even if the numberOfIterations are
reached without convergence. (Intended for use when --failureExitCode
0 ) (default: 0)

--failureExitCode <int>
If the fit fails, exit with this status code. (It can be used to
force a successfult exit status of (0) if the registration fails due
to reaching the maximum number of iterations. (default: -1)

--maximumStepSize <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.2)

--relaxationFactor <double>
Internal debugging parameter, and should probably never be used from
the command line. This will be removed in the future. (default: 0.5)

--useExplicitPDFDerivativesMode <AUTO|ON|OFF>
Using mode AUTO means OFF for BSplineDeformableTransforms and ON for
the linear transforms. The ON alternative uses more memory to
sometimes do a better job. (default: AUTO)

--useCachingOfBSplineWeightsMode <ON|OFF>
This is a 5x speed advantage at the expense of requiring much more
memory. Only relevant when transformType is BSpline. (default: ON)

--movingVolumeOrigin <std::vector<int>>
The coordinates of the origin of the moving image. This will
over-ride the information read from disk and is VERY DANGEROUS.
(default: 0,0,0)

--fixedVolumeOrigin <std::vector<int>>
The coordinates of the origin of the fixed image. This will over-ride
the information read from disk and is VERY DANGEROUS. (default: 0,0
,0)

--permitParameterVariation <std::vector<int>>
A bit vector to permit linear transform parameters to vary under
optimization. The vector order corresponds with transform parameters,
and beyond the end ones fill in as a default. For instance, you can
choose to rotate only in x (pitch) with 1,0,0; this is mostly for
expert use in turning on and off individual degrees of freedom in
rotation, translation or scaling without multiplying the number of
transform representations; this trick is probably meaningless when
tried with the general affine transform.

--studyID <std::string>
Identifier for the scanner encounter (MRQID), This will eventually be
removed. (default: ANON)

--patientID <std::string>
Identifier for the research subject, This will eventually be removed.
(default: ANON)

--numberOfMatchPoints <int>
the number of match points (default: 10)

--numberOfHistogramBins <int>
the number of histogram levels (default: 50)

-e, --histogramMatch
Histogram Match the input images. This is suitable for images of the
same modality that may have different absolute scales, but the same
overall intensity profile. (default: 0)

--medianFilterSize <std::vector<int>>
The radius for the optional MedianImageFilter preprocessing in all 3
directions. (default: 0,0,0)

--movingVolumeTimeIndex <int>
The index in the time series for the 3D moving image to fit, if
4-dimensional. (default: 0)

--fixedVolumeTimeIndex <int>
The index in the time series for the 3D fixed image to fit, if
4-dimensional. (default: 0)

--movingBinaryVolume <std::string>
Moving Image binary mask volume.

--fixedBinaryVolume <std::string>
Fixed Image binary mask volume.

--outputMovingVolumeROI <std::string>
The ROI automatically found in moving image.

--outputFixedVolumeROI <std::string>
The ROI automatically found in fixed image.

--maskProcessingMode <NOMASK|ROIAUTO|ROI>
What mode to use for using the masks. If ROIAUTO is choosen, then the
mask is implicitly defined using a otsu forground and hole filling
algorithm. The Region Of Interest mode (choose ROI) uses the masks to
define what parts of the image should be used for computing the
transform. (default: NOMASK)

--useWindowedSinc
Use windowedSinc interpolation to create output images. WARNING: This
will add 8 minutes to the interpolation of the final image of size
256x256x256. (default: 0)

--scaleOutputValues
If true, and the voxel values do not fit within the minimum and
maximum values of the desired outputVolumePixelType, then linearly
scale the min/max output image voxel values to fit within the min/max
range of the outputVolumePixelType. (default: 0)

--backgroundFillValue <double>
Background fill value for output image. (default: 0)

--outputVolumePixelType <float|short|ushort|int|uint|uchar>
The output image Pixel Type is the scalar datatype for representation
of the Output Volume. (default: float)

--outputVolume <std::string>
The (optional) output image for registration.

--strippedOutputTransform <std::string>
File name for the estimated transform, stripped of scaling, to
register the moving image to the fixed image.

--outputTransform <std::string>
Filename to which save the estimated transform.

--maxBSplineDisplacement <double>
Sets the maximum allowed displacements in image physical coordinates
for BSpline control grid along each axis. A value of 0.0 indicates
that the problem should be unbounded. NOTE: This only constrains the
BSpline portion, and does not limit the displacement from the
associated bulk transform. This can lead to a substantial reduction
in computation time in the BSpline optimizer. (default: 0)

--splineGridSize <std::vector<int>>
The number of subdivisions of the BSpline Grid to be centered on the
image space. Each dimension must have at least 3 subdivisions for the
BSpline to be correctly computed. (default: 14,10,12)

--skewScale <double>
ScaleSkewVersor3D Skew compensation factor. Increase this to put more
skew in a ScaleSkewVersor3D search pattern. 1.0 works well with a
translationScale of 1000.0 (default: 1)

--reproportionScale <double>
ScaleVersor3D 'Scale' compensation factor. Increase this to put more
rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern. 1.0
works well with a translationScale of 1000.0 (default: 1)

--translationScale <double>
How much to scale up changes in position compared to unit rotational
changes in radians -- decrease this to put more rotation in the search
pattern. (default: 1000)

--minimumStepSize <std::vector<double>>
Each step in the optimization takes steps at least this big. When
none are possible, registration is complete. (default: 0.005)

--numberOfSamples <int>
The number of voxels sampled for mutual information computation.
Increase this for a slower, more careful fit. You can also limit the
sampling focus with ROI masks and ROIAUTO mask generation. (default:
100000)

--numberOfIterations <std::vector<int>>
The maximum number of iterations to try before failing to converge.
Use an explicit limit like 500 or 1000 to manage risk of divergence
(default: 1500)

--initialTransform <std::string>
Filename of transform used to initialize the registration.

--maskInferiorCutOffFromCenter <double>
For use with --initializeTransformMode CenterOfHead (and
--maskProcessingMode ROIAUTO): the cut-off below the image centers, in
millimeters, (default: 1000)

--initializeTransformMode <Off|MomentsOn|CenterOfHead|GeometryOn>
Determine how to initialize the transform center. GeometryOn on
assumes that the center of the voxel lattice of the images represent
similar structures. MomentsOn assumes that the center of mass of the
images represent similar structures. CenterOfHead attempts to use the
top of head and shape of neck to drive a center of mass estimate. Off
assumes that the physical space of the images are close, and that
centering in terms of the image Origins is a good starting point.
This flag is mutually exclusive with the initialTransform flag.
(default: Off)

--transformType <std::vector<std::string>>
Specifies one of the four rigid ITK 3D transform types -- or BSpline
-- to use in parameter optimization descent. BRAINSFit always
optimizes mutual information, but the kind of descent varies with the
transform type. The valid types are, Rigid, ScaleVersor3D,
ScaleSkewVersor3D, Affine, and BSpline. Specifiying more than one in
a comma separated list will initialize the next stage with the
previous results. (default: Rigid)

--movingVolume <std::string>
The moving image for registration by mutual information optimization.

--fixedVolume <std::string>
The fixed image for registration by mutual information optimization.

|[[Image:BRAINSFitUIl.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===
BRAINSFit depends on Slicer3 (for the SlicerExecutionModel support) and ITK.
===Tests===
TODO: Link to BRAINS3 and/or Slicer3 dashboard tests.
===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

File:BRAINSFitUI.png

2010-05-06T19:19:25Z

KentWilliams:

Modules:BRAINSFit

2010-05-06T18:58:53Z

KentWilliams:

Modules:BRAINSFit

2010-05-06T18:57:03Z

KentWilliams:

Modules:BRAINSFit

2010-05-06T18:52:42Z

KentWilliams:

Documentation/3.6

2010-05-06T18:38:07Z

KentWilliams:

=Documentation Draft notes=
Key for flagged modules below:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module. If you're not sure how/where to add the link and module description:
* for command line modules, see other xml files (such as that for the GradientAnisotropicDiffusion Module) for an example of how to add documentation and links to wiki help.
* for interactive modules, see other modules in Base/GUI for an example.

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

=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 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 and the following [[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]]

=Main GUI=

*[[Image:WeakDoc.png]][[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)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=

==Core==
*[[Image:WeakDoc.png]][[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]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[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.
*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).
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
** [[Image:MissingOrStaleDoc.png]][[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 theh 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:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (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|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

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

==Diffusion MRI==
*Diffusion MRI Welcome Module
* DWI filtering
**[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
**[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
**[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
* Diffusion tensor utilities
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
* Resampling
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
* Tractography
**[[Image:MissingOrStaleDocLink.png]][[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)

==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==
*[[Registration:Resampling|'''Overview of Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[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)
*[[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Image:MissingOrStaleDoc.png]][[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Scalar Volume Batch Make]] (Julien Finet)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*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
**[[Image:WeakDoc.png]][[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)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python 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)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[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)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

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

==Slicer Extensions==

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* 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 those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* 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) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@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) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[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-3.5|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'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

=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]]

'''Modules'''
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

'''Requirements for Modules'''
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

Modules:BRAINSDemonWarp

2010-05-06T16:16:06Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:BRAINSDemonWarpForm.png|thumb|280px|User Interface]]
|}

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

Type: Interactive

Category: Registration

===Authors, Collaborators & Contact===
* Original Author: Tom Vercauteren : Institut National de Recherche En Informatique Et En Automatique
* Contributor: Gregory Harris : University of Iowa
* Contributor: Hans J. Johnson : University of Iowa
* Contributor: Kent WIlliams : University of Iowa
* Contact: Hans J. Johnson hans-johnson@uiowa.edu

===Module Description===
BRAINSDemonWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms.
== Usage ==
The module requires a template image and a target image and registers the template (moving) image onto the target (fixed) image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image file types supported by that library.
===Use Cases, Examples===
The inputs to the BrainDemonsWarp program are the target image, the template image and the optional parameters. These parameters define the arguments for histogram matching and multi resolution registration. The outputs are the deformation field, output image, checkerboard image of the output and the fixed image and the x,y,z displacement vectors. If we specify debug option we can get the outputs at different stages. The filter is templated over the input image type, real image type and the output image types. We implement the algorithm by parsing the input, preprocessing them and registering the processed images.

# Parsing - The images are initialized by the ValidationInputParser. This function reads in the arguments from the parameter file. It sets the histogram bins, match points, number of levels in the multi resolution registration, shrink factors and number of iterations at each levels. If the orientations of the images are different it sets the orientation of the moving image to that of the fixed image.
# PreProcessing - In the next step the DemonsPreProcessor preprocesses the images by resampling the template image to target image space. The intensity mismatch problem is solved by histogram matching the images. Histogram matching is done only if the command line option -e is set. ItkHistogramMatchingImageFilter is used to perform this function. Another important step in preprocessing is skull stripping. Skull stripping is done only if the command line option -maskProcessingMode is set to BOBF. We have written an itk filter, named itkBOBFFilter for this purpose. This filter takes in an input image and a whole brain mask and outputs a Brain Only Background Filled(BOBF) image. The non-brain parts in the image are filled with the user specified background value. All computations are performed in the precision of ﬂoat data.
# Registration - The resulting moving Image and the fixed image are given as inputs to the demons registrator.It uses the MultiResolutionPDEDeformableRegistration filter with NN extrapolation as interpolator and implements the demons deformable algorithm by computing the deformation field which will map a moving image onto a fixed image. It is assumed that the vector elements behave like ﬂoating point scalars. Each vector in the deformation field represent the distance between a geometric point in the input space and a point in the output space. The output image is generated by warping the input image with the deformation field using the ItkWarpImageFilter. WarpImageFilter warps an existing image with respect to a given deformation field. Typically the mapped position does not correspond to an integer pixel position in the input image. Interpolation via an image function is used to compute values at non-integer positions. We have used the LinearInterpolateImageFunction for our application. To write the output image we cast the image to the user specified output pixel type.

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

== Development ==

===Notes from the Developer(s)===

===Dependencies===

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/BRAINSTools/BRAINSDemonWarp/ BRAINSDemonWarp]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:BRAINSDemonWarp

2010-05-06T16:14:22Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:BRAINSDemonWarpForm.png|thumb|280px|User Interface]]
|}

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

Type: Interactive

Category: Registration

===Authors, Collaborators & Contact===
* Original Author: Tom Vercauteren : Institut National de Recherche En Informatique Et En Automatique
* Contributor: Gregory Harris : University of Iowa
* Contributor: Hans J. Johnson : University of Iowa
* Contributor: Kent WIlliams : University of Iowa
* Contact: Hans J. Johnson hans-johnson@uiowa.edu

===Module Description===
BRAINSDemonWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms.
== Usage ==
The module requires a template image and a target image and registers the template (moving) image onto the target (fixed) image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image file types supported by that library.
===Use Cases, Examples===
The inputs to the BrainDemonsWarp program are the target image, the template image and the optional parameters. These parameters define the arguments for histogram matching and multi resolution registration. The outputs are the deformation field, output image, checkerboard image of the output and the fixed image and the x,y,z displacement vectors. If we specify debug option we can get the outputs at different stages. The filter is templated over the input image type, real image type and the output image types. We implement the algorithm by parsing the input, preprocessing them and registering the processed images.

# Parsing - The images are initialized by the ValidationInputParser. This function reads in the arguments from the parameter file. It sets the histogram bins, match points, number of levels in the multi resolution registration, shrink factors and number of iterations at each levels. If the orientations of the images are different it sets the orientation of the moving image to that of the fixed image.
# PreProcessing - In the next step the DemonsPreProcessor preprocesses the images by resampling the template image to target image space. The intensity mismatch problem is solved by histogram matching the images. Histogram matching is done only if the command line option -e is set. ItkHistogramMatchingImageFilter is used to perform this function. Another important step in preprocessing is skull stripping. Skull stripping is done only if the command line option -maskProcessingMode is set to BOBF. We have written an itk filter, named itkBOBFFilter for this purpose. This filter takes in an input image and a whole brain mask and outputs a Brain Only Background Filled(BOBF) image. The non-brain parts in the image are filled with the user specified background value. All computations are performed in the precision of ﬂoat data.
# Registration - The resulting moving Image and the fixed image are given as inputs to the demons registrator.It uses the MultiResolutionPDEDeformableRegistration filter with NN extrapolation as interpolator and implements the demons deformable algorithm by computing the deformation field which will map a moving image onto a fixed image. It is assumed that the vector elements behave like ﬂoating point scalars. Each vector in the deformation field represent the distance between a geometric point in the input space and a point in the output space. The output image is generated by warping the input image with the deformation field using the ItkWarpImageFilter. WarpImageFilter warps an existing image with respect to a given deformation field. Typically the mapped position does not correspond to an integer pixel position in the input image. Interpolation via an image function is used to compute values at non-integer positions. We have used the LinearInterpolateImageFunction for our application. To write the output image we cast the image to the user specified output pixel type.

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

== Development ==

===Notes from the Developer(s)===

===Dependencies===

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/BRAINSTools/BRAINSDemonWarp/]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:BRAINSDemonWarp

2010-05-06T14:20:49Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:BRAINSDemonWarpForm.png|thumb|280px|User Interface]]
|}

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

Type: Interactive

Category: Registration

===Authors, Collaborators & Contact===
* Original Author: Tom Vercauteren : Institut National de Recherche En Informatique Et En Automatique
* Contributor: Gregory Harris : University of Iowa
* Contributor: Hans J. Johnson : University of Iowa
* Contributor: Kent WIlliams : University of Iowa
* Contact: Hans J. Johnson hans-johnson@uiowa.edu

===Module Description===
BRAINSDemonWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms.
== Usage ==
The module requires a template image and a target image and registers the template (moving) image onto the target (fixed) image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image file types supported by that library.
===Use Cases, Examples===
The inputs to the BrainDemonsWarp program are the target image, the template image and the optional parameters. These parameters define the arguments for histogram matching and multi resolution registration. The outputs are the deformation field, output image, checkerboard image of the output and the fixed image and the x,y,z displacement vectors. If we specify debug option we can get the outputs at different stages. The filter is templated over the input image type, real image type and the output image types. We implement the algorithm by parsing the input, preprocessing them and registering the processed images.

# Parsing - The images are initialized by the ValidationInputParser. This function reads in the arguments from the parameter file. It sets the histogram bins, match points, number of levels in the multi resolution registration, shrink factors and number of iterations at each levels. If the orientations of the images are different it sets the orientation of the moving image to that of the fixed image.
# PreProcessing - In the next step the DemonsPreProcessor preprocesses the images by resampling the template image to target image space. The intensity mismatch problem is solved by histogram matching the images. Histogram matching is done only if the command line option -e is set. ItkHistogramMatchingImageFilter is used to perform this function. Another important step in preprocessing is skull stripping. Skull stripping is done only if the command line option -maskProcessingMode is set to BOBF. We have written an itk filter, named itkBOBFFilter for this purpose. This filter takes in an input image and a whole brain mask and outputs a Brain Only Background Filled(BOBF) image. The non-brain parts in the image are filled with the user specified background value. All computations are performed in the precision of ﬂoat data.
# Registration - The resulting moving Image and the fixed image are given as inputs to the demons registrator.It uses the MultiResolutionPDEDeformableRegistration filter with NN extrapolation as interpolator and implements the demons deformable algorithm by computing the deformation field which will map a moving image onto a fixed image. It is assumed that the vector elements behave like ﬂoating point scalars. Each vector in the deformation field represent the distance between a geometric point in the input space and a point in the output space. The output image is generated by warping the input image with the deformation field using the ItkWarpImageFilter. WarpImageFilter warps an existing image with respect to a given deformation field. Typically the mapped position does not correspond to an integer pixel position in the input image. Interpolation via an image function is used to compute values at non-integer positions. We have used the LinearInterpolateImageFunction for our application. To write the output image we cast the image to the user specified output pixel type.

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input Image Files'''
** '''Moving Image Volume -- image to register'''
** '''Fixed Image Volume -- target for registration'''
* '''Output Files'''
** '''Output Image Volume -- transformed moving volume'''
** '''Output Deformation Field Volume -- each voxel is a vector defining translation of voxels from the moving image to fixed image space'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:BRAINSDemonWarpForm.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:BRAINSDemonWarp

2010-05-05T21:40:00Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:BRAINSDemonWarpForm.png|thumb|280px|User Interface]]
|}

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

Type: Interactive

Category: Registration

===Authors, Collaborators & Contact===
* Original Author: Tom Vercauteren : Institut National de Recherche En Informatique Et En Automatique
* Contributor: Gregory Harris : University of Iowa
* Contributor: Hans J. Johnson : University of Iowa
* Contributor: Kent WIlliams : University of Iowa
* Contact: Hans J. Johnson hans-johnson@uiowa.edu

===Module Description===
BRAINSDemonWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms.
== Usage ==
The module requires a template image and a target image and registers the template (moving) image onto the target (fixed) image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image file types supported by that library.
===Use Cases, Examples===
The inputs to the BrainDemonsWarp program are the target image, the template image and the optional parameters. These parameters define the arguments for histogram matching and multi resolution registration. The outputs are the deformation field, output image, checkerboard image of the output and the fixed image and the x,y,z displacement vectors. If we specify debug option we can get the outputs at different stages. The filter is templated over the input image type, real image type and the output image types. We implement the algorithm by parsing the input, preprocessing them and registering the processed images.

# Parsing - The images are initialized by the ValidationInputParser. This function reads in the arguments from the parameter file. It sets the histogram bins, match points, number of levels in the multi resolution registration, shrink factors and number of iterations at each levels. If the orientations of the images are different it sets the orientation of the moving image to that of the fixed image.
# PreProcessing - In the next step the DemonsPreProcessor preprocesses the images by resampling the template image to target image space. The intensity mismatch problem is solved by histogram matching the images. Histogram matching is done only if the command line option -e is set. ItkHistogramMatchingImageFilter is used to perform this function. Another important step in preprocessing is skull stripping. Skull stripping is done only if the command line option -maskProcessingMode is set to BOBF. We have written an itk filter, named itkBOBFFilter for this purpose. This filter takes in an input image and a whole brain mask and outputs a Brain Only Background Filled(BOBF) image. The non-brain parts in the image are filled with the user specified background value. All computations are performed in the precision of ﬂoat data.
# Registration - The resulting moving Image and the fixed image are given as inputs to the demons registrator.It uses the MultiResolutionPDEDeformableRegistration filter with NN extrapolation as interpolator and implements the demons deformable algorithm by computing the deformation field which will map a moving image onto a fixed image. It is assumed that the vector elements behave like ﬂoating point scalars. Each vector in the deformation field represent the distance between a geometric point in the input space and a point in the output space. The output image is generated by warping the input image with the deformation field using the ItkWarpImageFilter. WarpImageFilter warps an existing image with respect to a given deformation field. Typically the mapped position does not correspond to an integer pixel position in the input image. Interpolation via an image function is used to compute values at non-integer positions. We have used the LinearInterpolateImageFunction for our application. To write the output image we cast the image to the user specified output pixel type.

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:BRAINSDemonWarpForm.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

File:BRAINSDemonWarpForm.png

2010-05-05T21:00:01Z

KentWilliams: uploaded a new version of "File:BRAINSDemonWarpForm.png"

Modules:BRAINSDemonWarp

2010-05-05T20:49:40Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:BRAINSDemonWarpForm.png|thumb|280px|User Interface]]
|}

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

Type: Interactive

Category: Registration

===Authors, Collaborators & Contact===
* Author: Tom Vercauteren : Institut National de Recherche En Informatique Et En Automatique
* Contributor: Hans J. Johnson : University of Iowa
* Contributor2: Kent WIlliams : University of Iowa
* Contact: Hans J. Johnson hans-johnson@uiowa.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==
BRAINSDemonWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library.
===Use Cases, Examples===
The inputs to the BrainDemonsWarp program are the target image, the template image and the optional parameters. These parameters define the arguments for histogram matching and multi resolution registration. The outputs are the deformation field, output image, checkerboard image of the output and the fixed image and the x,y,z displacement vectors. If we specify debug option we can get the outputs at different stages. The filter is templated over the input image type, real image type and the output image types. We implement the algorithm by parsing the input, preprocessing them and registering the processed images.

# Parsing - The images are initialized by the ValidationInputParser. This function reads in the arguments from the parameter file. It sets the histogram bins, match points, number of levels in the multi resolution registration, shrink factors and number of iterations at each levels. If the orientations of the images are different it sets the orientation of the moving image to that of the fixed image.
# PreProcessing - In the next step the DemonsPreProcessor preprocesses the images by resampling the template image to target image space. The intensity mismatch problem is solved by histogram matching the images. Histogram matching is done only if the command line option -e is set. ItkHistogramMatchingImageFilter is used to perform this function. Another important step in preprocessing is skull stripping. Skull stripping is done only if the command line option -maskProcessingMode is set to BOBF. We have written an itk filter, named itkBOBFFilter for this purpose. This filter takes in an input image and a whole brain mask and outputs a Brain Only Background Filled(BOBF) image. The non-brain parts in the image are filled with the user specified background value. All computations are performed in the precision of ﬂoat data.
# Registration - The resulting moving Image and the fixed image are given as inputs to the demons registrator.It uses the MultiResolutionPDEDeformableRegistration filter with NN extrapolation as interpolator and implements the demons deformable algorithm by computing the deformation field which will map a moving image onto a fixed image. It is assumed that the vector elements behave like ﬂoating point scalars. Each vector in the deformation field represent the distance between a geometric point in the input space and a point in the output space. The output image is generated by warping the input image with the deformation field using the ItkWarpImageFilter. WarpImageFilter warps an existing image with respect to a given deformation field. Typically the mapped position does not correspond to an integer pixel position in the input image. Interpolation via an image function is used to compute values at non-integer positions. We have used the LinearInterpolateImageFunction for our application. To write the output image we cast the image to the user specified output pixel type.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:BRAINSDemonWarpForm.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

File:BRAINSDemonWarpForm.png

2010-05-05T20:46:01Z

KentWilliams:

Modules:BRAINSDemonWarp

2010-05-05T19:15:21Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

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

Type: Interactive

Category: Registration

===Authors, Collaborators & Contact===
* Author: Tom Vercauteren : Institut National de Recherche En Informatique Et En Automatique
* Contributor: Hans J. Johnson : University of Iowa
* Contributor2: Kent WIlliams : University of Iowa
* Contact: Hans J. Johnson hans-johnson@uiowa.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==
BRAINSDemonWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library.
===Use Cases, Examples===
The inputs to the BrainDemonsWarp program are the target image, the template image and the optional parameters. These parameters define the arguments for histogram matching and multi resolution registration. The outputs are the deformation field, output image, checkerboard image of the output and the fixed image and the x,y,z displacement vectors. If we specify debug option we can get the outputs at different stages. The filter is templated over the input image type, real image type and the output image types. We implement the algorithm by parsing the input, preprocessing them and registering the processed images.

# Parsing - The images are initialized by the ValidationInputParser. This function reads in the arguments from the parameter file. It sets the histogram bins, match points, number of levels in the multi resolution registration, shrink factors and number of iterations at each levels. If the orientations of the images are different it sets the orientation of the moving image to that of the fixed image.
# PreProcessing - In the next step the DemonsPreProcessor preprocesses the images by resampling the template image to target image space. The intensity mismatch problem is solved by histogram matching the images. Histogram matching is done only if the command line option -e is set. ItkHistogramMatchingImageFilter is used to perform this function. Another important step in preprocessing is skull stripping. Skull stripping is done only if the command line option -maskProcessingMode is set to BOBF. We have written an itk filter, named itkBOBFFilter for this purpose. This filter takes in an input image and a whole brain mask and outputs a Brain Only Background Filled(BOBF) image. The non-brain parts in the image are filled with the user specified background value. All computations are performed in the precision of ﬂoat data.
# Registration - The resulting moving Image and the fixed image are given as inputs to the demons registrator.It uses the MultiResolutionPDEDeformableRegistration filter with NN extrapolation as interpolator and implements the demons deformable algorithm by computing the deformation field which will map a moving image onto a fixed image. It is assumed that the vector elements behave like ﬂoating point scalars. Each vector in the deformation field represent the distance between a geometric point in the input space and a point in the output space. The output image is generated by warping the input image with the deformation field using the ItkWarpImageFilter. WarpImageFilter warps an existing image with respect to a given deformation field. Typically the mapped position does not correspond to an integer pixel position in the input image. Interpolation via an image function is used to compute values at non-integer positions. We have used the LinearInterpolateImageFunction for our application. To write the output image we cast the image to the user specified output pixel type.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:BRAINSDemonWarp

2010-05-05T18:23:53Z

KentWilliams:

Modules:BRAINSDemonWarp

2010-05-05T16:54:43Z

KentWilliams:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}

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

Type: Interactive

Category: Registration

===Authors, Collaborators & Contact===
* Author: Tom Vercauteren : Institut National de Recherche En Informatique Et En Automatique
* Contributor: Hans J. Johnson : University of Iowa
* Contributor2: Kent WIlliams : University of Iowa
* Contact: Hans J. Johnson hans-johnson@uiowa.edu

===Module Description===
Overview of what the module does goes here.

== Usage ==
BrainDemonsWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library.
===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.