Slicer Wiki - User contributions [en]

Documentation/3.6

2010-05-05T21:41:13Z

Sylvain:

=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)
** [[Image:MissingOrStaleDoc.png]][[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)

Slicer3:Using3.4

2009-02-12T22:20:04Z

Sylvain: /* Who */

== What ==
Developer and interested users should get together to step through common usage activities to identify the punch list of issues that must be resolved for the slicer 3.4 release. This is primarily for debugging, although ideas for new features can be added to the bug tracker.

== When, Where ==
1:00 - 5:00 on Tuesday Feb 24, 2009 at the 1249 Boylston 2nd floor demo room.

== Use Scenarios to Review ==

* Loading Data
** Local data browsing
** DICOM Loading
*** directories
** Remote IO
* Fiducials
** loading, saving, managing lists, assign colors
* Colors
** load save LUT
** Pet lut
* Viewing, Comparing Volumes
* Undo/Redo
* Volume Rendering
** transfer function loading saving
* Label Map Editing
** island removal, removing non functional icons
* Building Models
* Saving and Restoring Scenes
** Cleaning of refs to things that were deleted
* Registration
**rigid, affine, non-rigid
**what is in and what is out
* Tensor Estimation
* Tractography
**stochastic, landmark roi
* Meshing
** reading and inflated freesurfer brain
* Tracking Changes
**test jacobian

== Who ==
(sign up if you plan to attend)
* Steve Pieper
* Ron Kikinis ([[Slicer3:UserFeedbackAndFeatureRequests#Slicer_3.4_Usability|Rons wishlist]])
* Nicole Aucoin
* Mark Anderson
* Haiying Liu
* Tina kapur
* Junichi Tokuda
* Doug Terry
* Lauren O'Donnell
* Sylvain Bouix

Modules:ResampleVolume2-Documentation

2008-09-16T14:33:17Z

Sylvain: /* References */

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===ResampleVolume2===

{|
|[[Image:ResampleVolume2.png|thumb|280px|Module with panels expanded]]
|[[Image:OriginalBrainWebImage.jpg|thumb|200px|Original Image [[#References|[1] ]] ]]
|[[Image:BrainWebImageTransformed.jpg|thumb|200px|Transformed Image]]
|}

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

Type: CLI

Category: Filtering

===Authors, Collaborators & Contact===
* Francois Budin
* Sylvain Bouix, PNL
* Contact: Francois Budin , budin[at]bwh[dot]harvard[dot]edu

===Module Description===
This module implements image and vector-image resampling through the use of ITK Transforms. It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is especially appropriate when one needs to resample an image and already knows the transform to apply to it. Its principal advantages resides in the fact that one can apply any kind of transform supported by ITK (rigid, affine and non-rigid) and can choose between the most commonly used interpolators.
* The transform can be passed as an ITK Transform file using the command line, or directly as a transform node in Slicer3. In the latter case, the transform can only be rigid or affine.
* It also allows changing the spacing, the orientation, the size and the origin of the image.

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

* '''Input/Output:''' Defines input and output files.
** ''Input volume'' is the volume to resample,
** ''Reference Volume'' (optional) is the volume used to set the sampling parameters (origin, spacing, orientation and dimensions). If it is not set, the input volume will be taken for reference.
** ''Output volume'' is the name of the output.
* '''Resampling Parameters:''' Sets the number of threads used to perform the resampling.
* '''Transform Parameters:''' if the transform to be applied is in the slicer mrml tree, one can select it here.
* '''Manual Transform:''' if no tranform is set in previous panel, one can enter his own transform
** ''Transform Matrix:'' a 12-parameter affine transformation manually. The first 9 numbers represent a linear transformation matrix in column-major order (where the column index varies the fastest), the last 3 are a translation.
** ''Transform:'' forces the transform to be of rigid or affine type (affine is default)
** ''Space:'' It should normally not be modified when using this module directly in Slicer3. It does not specify whether the matrix is expressed in LPS or RAS coordinate space but rather if everything is expressed in the same coordinate space. LPS means that everything is in the same space and RAS means that it is not the case. This option can be set to RAS if the given transform is in RAS coordinate space (respectively LPS) and the input volume is in LPS coordinate space (respectively RAS). '''Be careful''': When passing manually the transform, the coordinate space modification is directly applied on the given transform. However, when passing the transform through a file or a transform node, it is the input volume coordinate space that is modified and the transform is left unchanged (so that any kind of transform supported by ITK is also supported by this module). If one sets the output volume parameters manually, one has to pay attention to the fact that in that case the given parameters are considered to be in the transform coordinate space!!!
* '''Rigid/Affine Parameters:'''
** ''Rotation Point:'' uses a fiducial to set a point around which the rotation defined in the transform needs to be performed.
** ''Centered Transform:'' sets the center of the transformation to the center of the image.
** ''Inverse ITK Transformation:'' inverses the transformation before applying it to the image. The transform given to the module is from the output image to the input one. If one wants to specify a transform from the input image to the output image, one should use this flag. This option can only be used if the transform is rigid or affine.
* '''Interpolation Type:''' sets the type of interpolation kernel to either linear, nearest neighbor (nn), windowed sinc (ws), or b-spline (bs).
* '''Windowed Sinc Interpolate Function Parameters:''' selects the type window function for the sinc interpolation h=hamming, c=cosine, w=welch, l=lanczos, b=blackman. '''This is only relevant if one selects ws as the interpolation type'''.
* '''BSpline Interpolate Function Parameters:''' The spline order (only relevant if the selected interpolator is bs).
* '''Output Parameters:''' One can overwrite the reference volume parameters by setting manually the ''spacing'', ''size'', ''origin'' (as a fiducial), and ''direction matrix'' (also known as space directions) in column-major order.

== Development ==

===Dependencies===

None

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===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===

[http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/ link] to ResampleVolume2.

== More Information ==

===When Using the module in command line===
* The Transform can be given through an ITK Transform file. An example is given below.
#Insight Transform File V1.0
# Transform 0
Transform: AffineTransform_double_3_3
Parameters: 1.73205080756880 0.5 0 -0.5 .8660254037844 0 0 0 1.5 15 32 27
FixedParameters: 40 35 20

* '''Be Careful :''' The transform file must have an empty line after the fixed parameters
* The Fixed Parameters are the coordinates of the center of rotation
* The Parameters are written in the following format:
** The first 9 numbers represent a linear transformation matrix in column-major order (where the column index varies the fastest)
** The last 3 are a translation.
* A transform file may contain multiple transforms. The module will apply all of them.

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on the National Centers for Biomedical Computing can be obtained from [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics].

===References===
[http://www.itk.org/ItkSoftwareGuide.pdf ITK software guide]. Sections "6.9 Geometric Transformations", "8.8 Transforms" and "8.9 Interpolators".

Modules:ResampleVolume2-Documentation

2008-09-16T14:29:52Z

Sylvain: /* References */

Modules:ResampleVolume2-Documentation

2008-09-16T14:28:31Z

Sylvain:

Modules:ResampleVolume2-Documentation

2008-09-15T15:25:46Z

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

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ResampleVolume2.png|thumb|280px|Module with panels expanded]]
|}

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

Type: CLI

Category: Filtering

===Authors, Collaborators & Contact===
* Francois Budin
* Sylvain Bouix, PNL
* Contact: Francois Budin , budin[at]bwh[dot]harvard[dot]edu

===Module Description===
This module implements image and vector-image resampling through the use of itk Transforms.It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.

== Usage ==

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input/Output:''' Defines input and output files.
** ''Input volume'' is the volume to resample,
** ''Reference Volume'' (optional) is the volume used to set the sampling parameters (spacing, orientation and dimensions),
** ''Output volume'' is the name of the output.
* '''Resampling Parameters:''' Sets the number of threads used to perform the resmapling.
* '''Transform Parameters:''' if the transform to be applied is in the slicer mrml tree, on can select it here.
* '''Manual Transform:''' if no tranform is set in previous panel, one can enter his own transform
** ''Transform Matrix:'' a 12 parameter affine transformation manually. The first 9 numbers represent a linear transformation matrix, the last 3 are a translation.
** ''Transform:'' forces the transform to be of rigid or affine type (affine is default)
** ''Space:'' specifies whether the matrix is expressed in LPS or RAS coordinate space.
* '''Rigid/Affine Parameters:'''
** ''Rotation Point:'' uses a fiducial to set a point around which the rotation defined in the transform needs to be performed.
** ''Centered Transform:'' sets the center of the transformation to the center of the image.
** ''Inverse ITK Transformation:'' inverses the transformation before applying it to the image
* '''Interpolation Type:''' sets the type of interpolation kernel to either linear, nearest neighbor (nn), windowed sinc (ws), or b-spline (bs).
* '''Windowed Sinc Interpolate Function Parameters:''' selects the type window function for the sinc interpolation h=hamming, c=cosine, w=welch, l=lanczos, b=blackman. '''This is only relevant if one selects ws as the interpolation type'''.
* '''BSpline Interpolate Function Parameters:''' The spline order.
* '''Output Parameters:''' if no reference volume is given, one can set the ''spacing'', ''size'', ''origin'' (as a fiducial), and ''direction matrix'' (also known as space directions) manually.

== Development ==

===Dependencies===

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

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===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===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

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

Modules:ResampleVolume2-Documentation

2008-09-15T15:25:05Z

Sylvain: /* Module Name */

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ResampleVolume2.png|thumb|280px|Module with panels expanded]]
|}

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

Type: CLI

Category: Filtering

===Authors, Collaborators & Contact===
* Francois Budin
* Sylvain Bouix, PNL
* Contact: Francois Budin , budin[at]bwh[dot]harvard[dot]edu

===Module Description===
This module implements image and vector-image resampling through the use of itk Transforms.It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.

== Usage ==

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input/Output:''' Defines input and output files.
** ''Input volume'' is the volume to resample,
** ''Reference Volume'' (optional) is the volume used to set the sampling parameters (spacing, orientation and dimensions),
** ''output volume'' is the name of the output.
* '''Resampling Parameters:''' Sets the number of threads used to perform the resmapling.
* '''Transform Parameters:''' if the transform to be applied is in the slicer mrml tree, on can select it here.
* '''Manual Transform:''' if no tranform is set in previous panel, one can enter his own transform
** ''Transform Matrix:'' a 12 parameter affine transformation manually. The first 9 numbers represent a linear transformation matrix, the last 3 are a translation.
** ''Transform:'' forces the transform to be of rigid or affine type (affine is default)
** ''Space:'' specifies whether the matrix is expressed in LPS or RAS coordinate space.
* '''Rigid/Affine Parameters:'''
** ''Rotation Point:'' uses a fiducial to set a point around which the rotation defined in the transform needs to be performed.
** ''Centered Transform:'' sets the center of the transformation to the center of the image.
** ''Inverse ITK Transformation:'' inverses the transformation before applying it to the image
* '''Interpolation Type:''' sets the type of interpolation kernel to either linear, nearest neighbor (nn), windowed sinc (ws), or b-spline (bs).
* '''Windowed Sinc Interpolate Function Parameters:''' selects the type window function for the sinc interpolation h=hamming, c=cosine, w=welch, l=lanczos, b=blackman. '''This is only relevant if one selects ws as the interpolation type'''.
* '''BSpline Interpolate Function Parameters:''' The spline order.
* '''Output Parameters:''' if no reference volume is given, one can set the ''spacing'', ''size'', ''origin'' (as a fiducial), and ''direction matrix'' (also known as space directions) manually.

== Development ==

===Dependencies===

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

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===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===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

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

Modules:ResampleVolume2-Documentation

2008-09-15T15:23:20Z

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

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ResampleVolume2.png|thumb|280px|Module with panels expanded]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

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

Type: CLI

Category: Filtering

===Authors, Collaborators & Contact===
* Francois Budin
* Sylvain Bouix, PNL
* Contact: Francois Budin , budin[at]bwh[dot]harvard[dot]edu

===Module Description===
This module implements image and vector-image resampling through the use of itk Transforms.It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.

== Usage ==

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input/Output:''' Defines input and output files.
** ''Input volume'' is the volume to resample,
** ''Reference Volume'' (optional) is the volume used to set the sampling parameters (spacing, orientation and dimensions),
** ''output volume'' is the name of the output.
* '''Resampling Parameters:''' Sets the number of threads used to perform the resmapling.
* '''Transform Parameters:''' if the transform to be applied is in the slicer mrml tree, on can select it here.
* '''Manual Transform:''' if no tranform is set in previous panel, one can enter his own transform
** ''Transform Matrix:'' a 12 parameter affine transformation manually. The first 9 numbers represent a linear transformation matrix, the last 3 are a translation.
** ''Transform:'' forces the transform to be of rigid or affine type (affine is default)
** ''Space:'' specifies whether the matrix is expressed in LPS or RAS coordinate space.
* '''Rigid/Affine Parameters:'''
** ''Rotation Point:'' uses a fiducial to set a point around which the rotation defined in the transform needs to be performed.
** ''Centered Transform:'' sets the center of the transformation to the center of the image.
** ''Inverse ITK Transformation:'' inverses the transformation before applying it to the image
* '''Interpolation Type:''' sets the type of interpolation kernel to either linear, nearest neighbor (nn), windowed sinc (ws), or b-spline (bs).
* '''Windowed Sinc Interpolate Function Parameters:''' selects the type window function for the sinc interpolation h=hamming, c=cosine, w=welch, l=lanczos, b=blackman. '''This is only relevant if one selects ws as the interpolation type'''.
* '''BSpline Interpolate Function Parameters:''' The spline order.
* '''Output Parameters:''' if no reference volume is given, one can set the ''spacing'', ''size'', ''origin'' (as a fiducial), and ''direction matrix'' (also known as space directions) manually.

== Development ==

===Dependencies===

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

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===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===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

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

Modules:ResampleVolume2-Documentation

2008-09-15T14:40:00Z

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

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ResampleVolume2.png|thumb|280px|Module with panels expanded]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

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

Type: CLI

Category: Filtering

===Authors, Collaborators & Contact===
* Francois Budin
* Sylvain Bouix, PNL
* Contact: Francois Budin , budin[at]bwh[dot]harvard[dot]edu

===Module Description===
This module implements image and vector-image resampling through the use of itk Transforms.It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.

== Usage ==

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input/Output:''' Defines input and output files.
** ''Input volume'' is the volume to resample,
** ''Reference Volume'' (optional) is the volume used to set the sampling parameters (spacing, orientation and dimensions),
** ''output volume'' is the name of the output.
* '''Resampling Parameters:''' Sets the number of threads used to perform the resmapling.
* '''Transform Parameters:''' if the transform to be applied is in the slicer mrml tree, on can select it here.
* '''Manual Transform:''' if no tranform is set in previous panel, one can enter his own transform
** ''Transform Matrix:'' a 12 parameter affine transformation manually. The first 9 numbers represent a linear transformation matrix, the last 3 are a translation.
** ''Transform:'' forces the transform to be of rigid or affine type (affine is default)
** ''Space:'' specifies whether the matrix is expressed in LPS or RAS coordinate space.

== Development ==

===Dependencies===

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

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===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===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

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

Modules:ResampleVolume2-Documentation

2008-09-15T14:38:34Z

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

[[Documentation|Return to Slicer Documentation]]
__NOTOC__
===Module Name===
MyModule

{|
|[[Image:ResampleVolume2.png|thumb|280px|Module with panels expanded]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

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

Type: CLI

Category: Filtering

===Authors, Collaborators & Contact===
* Francois Budin
* Sylvain Bouix, PNL
* Contact: Francois Budin , budin[at]bwh[dot]harvard[dot]edu

===Module Description===
This module implements image and vector-image resampling through the use of itk Transforms.It can also handle diffusion weighted MRI image resampling. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions.

== Usage ==

===Examples, Use Cases & Tutorials===

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input/Output:''' Defines input and output files. '''Input volume''' is the volume to resample, '''Reference Volume''' (optional) is the volume used to set the sampling parameters (spacing, orientation and dimensions), '''output volume''' is the name of the output.
* '''Resampling Parameters:''' Sets the number of threads used to perform the resmapling.
* '''Transform Parameters:''' if the transform to be applied is in the slicer mrml tree, on can select it here.
* '''Manual Transform:'''
** ''Transform Matrix:'' if no tranform is set in previous panel, one can enter a 12 parameter affine transformation manually. The first 9 numbers represent a linear transformation matrix, the last 3 are a translation.
** ''Transform:'' forces the transform to be of rigid or affine type (affine is default)
** ''Space:'' specifies whether the matrix is expressed in LPS or RAS coordinate space.

== Development ==

===Dependencies===

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

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===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===

Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

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

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