Python Explode Volume Transform
Module Type & Category
Authors, Collaborators & Contact
- Luca Antiga: Orobix Srl & Mario Negri Institute
- Daniel Blezek: Mayo Clinic
- Contact: Luca Antiga, email@example.com
This Python module takes a volume in input, extracts its IJKToRAS transform by matrix manipulation, where IJK is the local (VTK-compatible) coordinate system, and generates an IJK-oriented volume in the MRML scene as a child of a IJKToRAS transform node.
Use Cases, Examples
- The module is appropriate when a CLI module can only handle non-oriented images (i.e. images oriented as the XYZ axes), like pure-VTK modules.
- The typical use is as follows: run a volume through this filter, use the output volume as input for the non-orientation-aware CLI module and place the output of this latter module under the IJKToRAS transform generated by the present module by using the MRML tree widget.
- Use case: you have data generated from a RAS-agnostic program (e.g. fiber tracts generated in Matlab) and you want to place them in your RAS oriented scene in Slicer. What you do is then to load the MR b0 volume with orientation "From file", explode its ijkToRAS Transform, load the fiber tracts and place them under the exploded transform in the MRML tree (note that you may have to invert the transform beforehand if what you move under the transform is a polydata, as in this case). You can then (optionally) right-click on the fiber tract nodes and choose "Harden transforms" in order to have the transform applied to the fiber points. At this point you can save them in RAS.
Quick Tour of Features and Use
Notes from the Developer(s)
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Source code & documentation
Links to the module's source code: