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| − | {{documentation/{{documentation/version}}/module-header}}
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| + | {{documentation/banner |
| − | {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
| + | | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/transforms.html This page has been moved to read-the-docs.] |
| − | {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
| + | | background-color = 8FBC8F }} |
| − | {{documentation/{{documentation/version}}/module-introduction-row}}
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| − | :'''Author(s)/Contributor(s):''' Alex Yarmarkovich (Isomics, SPL), Jean-Christophe Fillion-Robin (Kitware), Julien Finet (Kitware), Andras Lasso (PerkLab, Queen's), Franklin King (PerkLab, Queen's)<br>
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| − | :'''Acknowledgements:''' This work is part of the [http://www.na-mic.org/ National Alliance for Medical Image Computing] (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.<br>
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| − | :'''Contact:''' Alex Yarmarkovich, <email>alexy@bwh.harvard.edu</email><br>
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| − | {{documentation/{{documentation/version}}/module-introduction-row}}
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| − | {{documentation/{{documentation/version}}/module-introduction-logo-gallery
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| − | |{{collaborator|logo|isomics}}|{{collaborator|longname|isomics}}
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| − | |{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}
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| − | |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
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| − | |{{collaborator|logo|nac}}|{{collaborator|longname|nac}}
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| − | {{documentation/{{documentation/version}}/module-introduction-end}}
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| − | {{documentation/{{documentation/version}}/module-section|Module Description}}
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| − | {{documentation/{{documentation/version}}/module-description}}
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| − | Features:
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| − | * Short video demonstrating the main features: http://screencast.com/t/Z6dQVjK3m
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| − | * Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform
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| − | * Transform information displayed in the Transforms module (type of transform, basic properties)
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| − | * Transform visualization:
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| − | ** Built into the Transforms module
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| − | ** Three main modes: Glyphs (show an array of arrows, cones, spheres), Grid (show a deformed grid), or Contour (show isolines/isosurfaces for specified displacement magnitude values)
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| − | ** All transform types are supported (chains of transforms as well)
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| − | ** Visualization in the slice viewers
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| − | ** Visualization in the 3D viewers, in the specified region (region can be a slice viewer, a volume, or a ROI widget)
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| − | ** Real-time update: if the transform (or any visualization parameter) is changed then the visualization is updated immediately (interactive visualization while editing the transform)
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| − | ** Built-in colormap editor
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| − | * MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform
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| − | {{documentation/{{documentation/version}}/module-section|Use Cases}}
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| − | Most frequently Transform module is used for these scenarios:
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| − | * Manual Registration: You can insert a transformation node into your scene, and in the Data module drag a volume or a model under it,
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| − | making them children of the transformation node. After that any changes to the transformation matrix of this node will be applied to the display of children volumes and models.
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| − | * Visualize the displacement that transforms specify: Transforms can be visualized in both 2D and 3D views, as glyphs representing the displacement vectors as arrows, cones, or spheres; regular grids that are deformed by the transform; or contours that represent lines or surfaces where the displacement magnitude has a specific value.
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| − | * Apply transforms: You can dynamically transform a node by selecting them in the ''Transformable'' list and clicking the ''right arrow'' button. Whenever the transform changes, the transformed nodes are updated accordingly. The ''Harden Transform'' (its button is below the ''left arrow'' button) can be used for applying the transform to nodes permanently. Transforms themselves can be transformed, therefore chain of transforms can be constructed. Non-linear transforms can be concatenated too, but to to the lack of standard file format for storing concatenated inverted transforms, such composite non-linear transforms cannot be saved to file.
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| − | {{documentation/{{documentation/version}}/module-section|Tutorials}}
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| − | * Please use tutorial about [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training loading and viewing data].
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| − | {{documentation/{{documentation/version}}/module-section|Panels and their use}}
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| − | Transform editing and application:
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| − | {|
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| − | |-
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| − | | [[Image:TransformsModule-43.png|thumb|280px|Transforms module panel]]
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| − | | [[Image:QSlicerTransformsModule.png|thumb|660px|''LinearTransform'' applied to ''Meningioma2''<br>Rotations: IS 45º<br>Translations: LR -41mm, IS 36mm]]
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| − | |}
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| − | | |
| − | Transform display options:
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| − | {|
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| − | |-
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| − | | [[Image:GlyphArrow2d.png|thumb|280px|Glyph visualization (arrow, 2D): the arrow shows the displacement vector at the arrow starting point, projected to the slice]]
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| − | | [[Image:GlyphCone2d.png|thumb|280px|Glyph visualization (cone, 2D): the cone shows the displacement vector at the cone centerpoint, projected to the slice]]
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| − | | [[Image:GlyphSphere2d.png|thumb|280px|Glyph visualization (sphere, 2D): the circle diameter shows the displacement vector magnitude at the circle centerpoint]]
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| − | |-
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| − | | [[Image:GlyphArrow3dSlice.png|thumb|280px|Glyph visualization (arrow, 3D, slice region): the arrow shows the displacement vector at the arrow starting point]]
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| − | | [[Image:GlyphCone3dVolumeRoi.png|thumb|280px|Glyph visualization (cone, 3D, annotation ROI region): the cone shows the displacement vector at the cone centerpoint]]
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| − | | [[Image:GlyphSphere3dVolume.png|thumb|280px|Glyph visualization (sphere, 3D, volume region, with glyph magnitude filtering): the sphere diameter shows the displacement vector magnitude at the circle centerpoint]]
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| − | |-
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| − | | [[Image:Grid2d.png|thumb|280px|Grid visualization (2D): shows a regular grid, deformed by the displacement vector projected to the slice]]
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| − | | [[Image:Grid3dSlice.png|thumb|280px|Grid visualization (3D, slice region): shows a regular grid, deformed by the displacement vector]]
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| − | | [[Image:Grid3dVolume.png|thumb|280px|Grid visualization (3D, annotation ROI region): shows a regular grid, deformed by the displacement vector]]
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| − | |-
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| − | | [[Image:Contour2d.png|thumb|280px|Contour visualization (2D): iso-lines corresponding to selected displacement magnitude values]]
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| − | | [[Image:Contour3dVolume.png|thumb|280px|Grid visualization (3D, volume region): iso-surfaces corresponding to selected displacement magnitude values]]
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| − | |}
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| − | {{documentation/{{documentation/version}}/module-parametersdescription}}
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| − | {{documentation/{{documentation/version}}/module-section|Similar Modules}}
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| − | * Related modules: [[Documentation/{{documentation/version}}/Modules/Data|Data module]], [[:Category:Documentation/{{documentation/version}}/Modules/Registration|Registration modules]].
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| − | {{documentation/{{documentation/version}}/module-section|References}}
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| − | N/A
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| − | {{documentation/{{documentation/version}}/module-section|Information for Developers}}
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| − | ===Key [[Documentation/{{documentation/version}}/Developers/MRML|MRML]] nodes===
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| − | * [http://slicer.org/doc/html/classvtkMRMLTransformableNode.html vtkMRMLTransformableNode]: any node that can be transformed
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| − | * [http://slicer.org/doc/html/classvtkMRMLTransformNode.html vtkMRMLTransformNode]: it can store any linear or deformable transform or composite of multiple transforms
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| − | ** [http://slicer.org/doc/html/classvtkMRMLLinearTransformNode.html vtkMRMLLinearTransformNode]: Deprecated. The transform does exactly the same as vtkMRMLTransformNode but has a different class name, which are still used for showing only certain transform types in node selectors. In the future this class will be removed. A vtkMRMLLinearTransformNode may contain non-linear components after a non-linear transform is hardened on it. Therefore, to check linearity of a transform the vtkMRMLTransformNode::IsLinear() and vtkMRMLTransformNode::IsTransformToWorldLinear() and vtkMRMLTransformNode::IsTransformToNodeLinear() methods must be used instead of using vtkMRMLLinearTransformNode::SafeDownCast(transform)!=NULL.
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| − | ** [http://slicer.org/doc/html/classvtkMRMLBSplineTransformNode.html vtkMRMLBSplineTransformNode]: Deprecated. The transform does exactly the same as vtkMRMLTransformNode but has a different class name, which are still used for showing only certain transform types in node selectors. In the future this class will be removed.
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| − | ** [http://slicer.org/doc/html/classvtkMRMLGridTransformNode.html vtkMRMLGridTransformNode]: Deprecated. The transform does exactly the same as vtkMRMLTransformNode but has a different class name, which are still used for showing only certain transform types in node selectors. In the future this class will be removed.
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| − | ===Examples===
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| − | How to programmatically apply a transform to a transformable node:
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| − | vtkNew<[http://slicer.org/doc/html/classvtkMRMLTransformNode.html vtkMRMLTransformNode]> transformNode;
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| − | scene->AddNode(transformNode.GetPointer());
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| − | ...
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| − | vtkNew<vtkMatrix4x4> matrix;
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| − | ...
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| − | transform->SetMatrixTransformToParent( matrix.GetPointer() );
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| − | ...
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| − | vtkMRMLVolumeNode* transformableNode = ...; // or vtkMRMLModelNode*... | |
| − | transformableNode->SetAndObserveTransformNodeID( transformNode->GetID() );
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| − | Because a ''transform'' node is also a ''transformable'' node, it is possible to concatenate transforms with each others:
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| − | [http://slicer.org/doc/html/classvtkMRMLTransformNode.html vtkMRMLTransformNode*] transformNode = ...;
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| − | [http://slicer.org/doc/html/classvtkMRMLTransformNode.html vtkMRMLTransformNode*] transformNode2 = ...;
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| − | transformNode2->SetAndObserveTransformNodeID( transformNode->GetID() );
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| − | ...
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| − | transformable->SetAndObserveTransformNodeID( transformNode2->GetID() );
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| − | How to export the transform to as a displacement field (in a vector field volume)?
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| − | transformNode=slicer.util.getNode('LinearTransform_3')
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| − | referenceVolumeNode=slicer.util.getNode('MRHead')
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| − | slicer.modules.transforms.logic().CreateDisplacementVolumeFromTransform(transformNode, referenceVolumeNode, False)
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| − | How to visualize the displacement magnitude as a color volume?
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| − | transformNode=slicer.util.getNode('LinearTransform_3')
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| − | referenceVolumeNode=slicer.util.getNode('MRHead')
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| − | slicer.modules.transforms.logic().CreateDisplacementVolumeFromTransform(transformNode, referenceVolumeNode, True)
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| − | ===Transform files===
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| − | * Slicer stores tansform in VTK classes in memory but uses ITK transform IO classes to read/write transforms to files. ITK's convention is to use LPS coordinate system as opposed to RAS coordinate system in Slicer. Conversion between VTK and ITK transform classes are implemented in [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkITKTransformConverter.h vtkITKTransformConverter].
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| − | * ITK stores the transform in "image processing" convention, i.e., that transforms points from fixed to moving coordinate system. This transform is usable as is for resampling a moving image in the coordinate system of a fixed image. For transforming points and surface models to the fixed coordinate system, one needs the transform in the "computer graphics" convention, i.e., transform from moving to fixed coordinate system (which is the inverse of the "image processing" convention).
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| − | * Transform nodes in Slicer can store transforms in both "computer graphics" (when ToParent transform is set) and "image processing" way (when FromParent transform is set). When writing transform to ITK files, linear transforms are inverted as needed and written as an AffineTransform. Non-linear transforms cannot be inverted without losing information (in general), therefore if a non-linear transform is defined in "computer graphics" convention in Slicer then it is written to ITK file using a "Inverse" transform types (e.g., InverseDisplacementFieldTransform instead of DisplacementFieldTransform). Definition of the inverse classes are available in [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkITKTransformInverse.h vtkITKTransformInverse]. The inverse classes are only usable for file IO, because currently ITK does not provide generic inverse computation method. Options to manage inverse transforms:
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| − | ** Create VTK transforms from ITK transforms: VTK transforms can compute their inverse, transform can be changed dynamically, the inverse will be always updated automatically in real-time (this approach is used by Slicer)
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| − | ** Invert transform in ITK statically: by converting to displacement field and inverting the displacement field; whenever the forward transform changes, the complete inverse transform has to be computed again (which is typically very time consuming)
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| − | ** Avoid inverse non-linear transforms: make sure that non-linear transforms are only set as FromParent
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| − | * Transforms module in Slicer shows linear transform matrix values in RAS coordinate system, according to "computer graphics" convention. Therefore to retrieve the same values from an ITK transforms as shown in Slicer GUI, one has to multiply the ITK transform by the matrix [-1,0,0,0; 0,-1,0,0; 0,0,1,0; 0,0,0,1] and invert the matrix.
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| − | ===Events===
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| − | When a transform node is observed by a transformable node, [http://slicer.org/doc/html/classvtkMRMLTransformableNode.html#ace1c30fc9df552543f00d51a20c038a6a4993bf6e23a6dfc138cb2efc1b9ce43b vtkMRMLTransformableNode::TransformModifiedEvent] is fired on the transformable node at observation time.
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| − | Anytime a transform is modified, vtkCommand::ModifiedEvent is fired on the transform node and [http://slicer.org/doc/html/classvtkMRMLTransformableNode.html#ace1c30fc9df552543f00d51a20c038a6a4993bf6e23a6dfc138cb2efc1b9ce43b vtkMRMLTransformableNode::TransformModifiedEvent] is fired on the transformable node.
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