I am doing the example from the Slicer Sequence Registration Module found online ( https://github.com/moselhy/SlicerSequenceRegistration ). I can visualize the results but how do I export them? How do I know how many nodes I have and how do I export their positions? Can you fit an equation to the de…

[image] miniBin: used the nrrdread.m file but it could not recognize the file It should work. If there was a problem then it msut be something trivial to fix. Maybe due to some minor syntax difference between Matlab versions. What error message did you get exactly? Unless you are near the en…

Thanks for the clarifications. I have succeeded in reading 4D transform using nrrdread.m you provided. But I don’t quite understand that “Displacement vector elements are defined in RAS coordinates in Slicer” and “for now you can do this yourself by inverting the sign of the first two components of …

Slicer can compute for you the displacement at each surface mesh point and save it in the mesh: after you exported the displacement field to image volume in Transforms module, go to “Probe volume with model” module to compute displacement of each model point and save it in the model as point data. T…

Thanks for the extended help. I think I will make the transition to python soon and will try to implement the whole workflow in python environment. Now I have got modified displacement field calculated by fem and imported it back to slicer as transform (.nrrd format using nrrdwrite.m ). I wonder if …

[image] labixin: I wonder if I have a contour/segment in moving image, can I apply transform to get a deformed one in fixed image? You can load the displacement field as a Transform (in Add data dialog, choose “Transform” in Description column) and apply it to any node (image, segment, etc.) …

[image] lassoan: What may be confusing is that Slicer stores elements in RAS coordinates, while the geometry of image saved to file is specified in LPS. Displacement vector elements are defined in RAS coordinates in Slicer and when we save a vector volume from Slicer, we do not alter the stored …

Transforms are written and read as LPS. Since Slicer uses RAS internally, there is an automatic conversion between RAS<->LPS when reading/writing a transform file. Vector volumes can store color, displacements, etc. in their voxels and they are read/written to file without any modification. If you…

[image] lassoan: If you export a transform to a vector volume in Transforms module then vectors will contain displacements in RAS coordinate system and since there is no conversion during read/write to file, if you save this volume, then the resulting file will contain displacement vectors in RA…

Image grid (origin, spacing, axis directions) is always saved as LPS. Vector components in the voxel data are saved as is (if it was RAS in Slicer then it is RAS in the file, too).

Thanks a lot @lassoan for your answer which sounds certain (indeed Image grid is saved LPS which is consistent to what I see). Just Disp grid is also LPS as it is align with the LPS image (used Paraview to verify). Perhaps I should reflect my testing procedure, maybe I made a mistake somewhere… Will…

Paraview completely ignores image axis directions, so it cannot be used for verification. What are you trying to achieve? What is your current workflow?

Registration Deformation Export

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Registration Deformation Export

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