I have image data in point cloud format (4 columns: x,y,z,intensity). How can I import this volume, or convert it to a format I can import into Slicer? Any help would be most appreciated!

Slicer could not load the .vtk file, as no SCALAR data was specified for point data. You can load the data manually using the Python console like this: # Read data set reader=vtk.vtkStructuredPointsReader() reader.SetFileName("test14.vtk") reader.Update() img=reader.GetOutput() # Set active point s…

Can you update the software that writes the file to use a standard file format that VTK understands - such as .vtk or .vtp? For example a .vtk file that contains point coordinates, normals, and a custom scalar (RandomPointScalars) looks like this: # vtk DataFile Version 4.0 vtk output ASCII DATASE…

Yes; it’s actually data that’s processed in Paraview (voxel data as a rectilinear grid). I can export it from Paraview as .vtk, .vtu, and so on, but once I import that into Slicer, it becomes a “model” with no signal information, and I would like it to import it as a “volume” so I can use Gaussian …

If you have a surface mesh then you can load it into Slicer as a model and import as a segment using Segmentations module. To edit in Segment Editor, you need to select a Master volume to define image resolution and axes. If you don’t have any volume then load any of the sample volumes and resize&re…

If you have volumetric mesh in Paraview, then convert it to an image using Resample to image filter and save it as a Meta Image (.mha or .mhd) file. Note that in general Slicer is much better suited for medical image analysis, processing, and visualization than Paraview, as Slicer is primarily deve…

Can I “resample a model to image” in Slicer? Doing so works in Paraview, but saving the result as a .mhd causes Paraview v5.4 to crash, on both Mac and PC. The main issue I’m still having with Slicer is that I can’t (or don’t know how to) use the Gaussian blur module in Slicer if my data is import…

Can you describe what you would like to do overall? Most likely you can do everything in Slicer and then you don’t have to worry about these conversions (Slicer can probably do all processing that you need while keeping your data as image or segmentation).

Sure; the program I’m using creates voxel data output as cells in a .vtk rectilinear grid. For example: vtk DataFile Version 3.0 vtk_output ASCII DATASET RECTILINEAR_GRID DIMENSIONS 51 101 41 X_COORDINATES 51 float -2.0000E+00 -1.9200E+00 -1.8400E+00 … Y_COORDINATES 101 float -4.5000E+00 -…

[image] Hamburgerfinger: the program I’m using creates voxel data output as cells in a .vtk rectilinear grid Maybe you could fix that program then. A vtk rectilinear grid is not a volume (vtkImageData), as in a rectilinear grid, spacing along each axis may vary arbitrarily, while in a volume,…

Unfortunately I’m not a programmer. But, I can save my file as vtkImageData in Paraview, but it still won’t import as a volume into Slicer. For example: 0 0 0 0 0 0 0 0 0 0 0 0 ... Isn’t this the same as “structured points”?

What software generates that file that contains the volume as.vtk rectilinear grid? Is there a particular reason why that software does not save the volume as an image (.vtk file with DATASET STRUCTURED_POINTS inside; .vti file; .nrrd or .mha file…)? You should be able to convert volumetric mesh (s…

Import point cloud data

Support

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Import point cloud data

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