Converting a STL file to nifti

Support
1

Hello Guys,

I am trying to convert an stl file to nifti using Dicer.

I found the following: Conversation: Converting .stl files to binary label maps in .nii format using Python

I have tried to follow the instructions of Donnie Cameron.

However, when I give the command:

seg.SetReferenceImageGeometryParameterFromVolumeNode(referenceVolumeNode)

I get the error message:

Traceback (most recent call last):
  File "<console>", line 1, in <module>
TypeError: SetReferenceImageGeometryParameterFromVolumeNode argument 1: method requires a VTK object

Similarly: If I follow Andras Lasso script and give the command:

outputLabelmapVolumeNode = 
slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')

I also get the error:

Traceback (most recent call last):
  File "<console>", line 1, in <module>
TypeError: ExportVisibleSegmentsToLabelmapNode argument 1: method requires a VTK object

Does anyone know what do I do wrong?

Best,
Yaron

2

See complete example in the script repository.

3

Dear Andras,

Thanks for your reply. I have tried to follow the script for converting stl to TIFF images but still get error messages. In particular, the command

inputModel.GetBounds(bounds)

returns the error message:

Traceback (most recent call last):
  File "<console>", line 1, in <module>
AttributeError: 'bool' object has no attribute 'GetBounds'

Similarly, the command:
slicer.modules.segmentations.logic().ImportModelToSegmentationNode(inputModel, seg)
Returns the error message:

Traceback (most recent call last):
  File "<console>", line 1, in <module>
TypeError: ImportModelToSegmentationNode argument 1: method requires a VTK object

To me it looks as if the method to load the stl file is the problematic one (inputModel = slicer.util.loadModel(inputModelFile) ).
Any idea how to solve it?

Thanks,
Yaron

4

The variable inputModel should contain a vtkMRMLModelNode and not a boolean

5

Dear Csaba,

The variable inputModel was set according to the script as:

inputModel = slicer.util.loadModel(inputModelFile)

Where inputModelFile was my path to my stl file.

And that created the boolean object.

Hence, I think that there is a problem in setting the stl as a vtk object in Slicer.
Any idea of how to do it?

Yaron

6

At this point this is regular Python programming.

If you see the documentation of the function you use you’ll see why you get a boolean:

>>> help(slicer.util.loadModel)
Help on function loadModel in module slicer.util:

loadModel(filename, returnNode=False)
    Load node from file.
    
    :param filename: full path of the file to load.
    :param returnNode: Deprecated.
    :return: loaded node (if multiple nodes are loaded then a list of nodes).
      If returnNode is True then a status flag and loaded node are returned.
7

Thanks.

Using the syntax:

[Status, inputModel] = slicer.util.loadModel(inputModelFile, returnNode=True)

indeed solved the problem.

Yaron

8

The API is changed in Slicer-4.11. By default we don’t use Boolean flag to indicate error anymore, but raise an exception instead. This allows simpler syntax of inputModel = slicer.util.loadModel(inputModelFile).

I would recommend to update to latest Slicer stable or preview release.