Transforms

Related MRML nodes

• vtkMRMLTransformableNode: any node that can be transformed

• vtkMRMLTransformNode: it can store any linear or deformable transform or composite of multiple transforms

  • 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) != nullptr.

  • 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.

  • 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.

Transform files

• Slicer stores transforms 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 (see the Coordinate systems page for details). Conversion between VTK and ITK transform classes are implemented in vtkITKTransformConverter.

• ITK stores the transform in resampling (a.k.a., 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 modeling (a.k.a. computer graphics) convention, i.e., transform from moving to fixed coordinate system (which is the inverse of the “image processing” convention).

• Transform nodes in Slicer can store transforms in both modeling (when “to parent” transform is set) and resampling way (when “from parent” 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 resampling convention in Slicer then it is written to ITK file using special “Inverse” transform types (e.g., InverseDisplacementFieldTransform instead of DisplacementFieldTransform). Definition of the inverse classes are available in vtkITKTransformInverse. The inverse classes are only usable for file IO, because currently ITK does not provide a generic inverse transform computation method. Options to manage inverse transforms in applications:

  • 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)

  • 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)

  • Avoid inverse non-linear transforms: make sure that non-linear transforms are only set as FromParent

• Transforms module in Slicer shows linear transform matrix values “to parent” (modeling convention) in RAS coordinate system. Therefore to retrieve the same values from an ITK transforms as shown in Slicer GUI, one has switch between RAS/LPS and modeling/resampling. See example here.

Displacement field files

Slicer can store displacement field transforms (or “grid transforms” in VTK naming convention) in 3D NRRD or NIFTI format; or sequence of transforms in NRRD format. Image file header fields are used to distinguish the displacement field transforms form regular images and specify how to correctly interpret these images as transforms.

NRRD

Required kinds:

• vector domain domain domain for a single 3D displacement field

• vector domain domain domain list for a sequence of displacement fields

Required custom intent_code:

• intent_code := 1006 Mirrors the NIfTI convention NIFTI_INTENT_DISPVECT, allowing ITK readers to detect displacement fields reliably.

Recommended measurement frame:

• measurement frame: (1,0,0) (0,1,0) (0,0,1) Use identity to state unambiguously that vector components are spatial and expressed in world space.

Optional usage hint (displacement field type):

• displacement field type := resampling | modeling

  • resampling (default): Interpret as a resampling transform (ITK convention, fixed to moving). In Slicer’s transform tree this corresponds to “from parent”.

  • modeling: Interpret as a modeling transform (useful for points/markups/models, moving to fixed). In Slicer’s transform tree this corresponds to “to parent”.

Per-item attributes for sequences (custom fields): Use these only when kinds includes a list axis.

• axis <A> index type := numeric | text Declares the type of the list-axis index values (affects parsing/sorting).

• axis <A> index values := <v0> <v1> ... <vN-1> Provides one index value per sequence item (values may be non-uniform or non-numeric). Provides the explicit index value for each sequence item, separated by spaces. Values can be arbitrary strings, stored using URL encoding.

• axis <A> item <I> <AttrName> := <AttrValue> Stores an arbitrary per-item attribute (becomes a node attribute on the corresponding MRML data node).

Where:

• <A> = the list axis index (the axis whose kinds entry is list)

• <I> = 0-based item index along the list axis

• Quote values that contain spaces per NRRD rules

• The count of index values must equal the size of the list axis

Note

In 3D + time sequences the vector axis is typically 0, followed by three spatial domain axes, and the list axis last. Do not assume a fixed number—always use the axis where kinds is list for <A>.

Example 3D displacement field file header

NRRD0005
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: double
dimension: 4
space: left-posterior-superior
sizes: 3 256 256 130
space directions: none (0,1,0) (0,0,-1) (-1.2999954223632812,0,0)
kinds: vector domain domain domain
endian: little
encoding: raw
space origin: (86.644897460937486,-133.92860412597656,116.78569793701172)
measurement frame: (1,0,0) (0,1,0) (0,0,1)
displacement field type:=resampling
intent_code:=1006

Example 3D+t displacement field sequence file header

NRRD0005
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: double
dimension: 5
space: left-posterior-superior
sizes: 3 88 160 72 14
space directions: none (0,1.5,0) (0.13855585501996717,0,-1.4935870497027235) (-1.4935870497027182,0,-0.13855585501997181) none
kinds: vector domain domain domain list
labels: "" "" "" "" "time"
units: "" "" "" "" "ms"
endian: little
encoding: gzip
space origin: (43.348771859606991,-103.34095001221,82.564098750818999)
measurement frame: (1,0,0) (0,1,0) (0,0,1)
axis 3 index type:=numeric
axis 3 index values:=18.551218032837 55.653656005859 92.756088256836 129.8585357666 166.96096801758 204.06340026855 241.16584777832 278.26824951172 315.37069702148 352.47314453125 389.57556152344 426.6780090332 463.78045654297 500.88287353516
displacement field type:=modeling
intent_code:=1006

The 3 in axis 3 index type and axis 3 index values fields refer to the 4th range axis (list).

NIfTI

• intent_code must be 1006 (NIFTI_INTENT_DISPVECT)

• Displacement vector components are stored in the RAS coordinate system

Events

When a transform node is observed by a transformable node, vtkMRMLTransformableNode::TransformModifiedEvent is fired on the transformable node at observation time. Anytime a transform is modified, vtkCommand::ModifiedEvent is fired on the transform node and vtkMRMLTransformableNode::TransformModifiedEvent is fired on the transformable node.

Examples

Examples for common operations on transform are provided in the script repository.