Dear all, I hope you’re doing well. I’ve spent the last week or two struggling to convert a large number of .stl files (~1,000) drawn in 3D Slicer 4.10.2 into .nii binary label maps using Python. The .stl data were derived from segmentations drawn on Dixon MRI .nii data that I’m using as the refere…

This works well for me: stl_file_name = ... output_file_name = ... reference_volume_path = ... referenceVolumeNode = slicer.util.loadVolume(reference_volume_path) segmentationNode = slicer.util.loadSegmentation(stl_file_name) outputLabelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLa…

The scripts are probably intended for latest Slicer Preview Release. Let us know if you have trouble making them work with that Slicer version.

Thanks very much for the tip. Using Slicer 4.11 I’m still getting empty .nii volumes with the script above, but I’ll have another go at the code from the script repository and I’ll report back.

Just to give some helpful context, using the ‘Model to LabelMap’ tool in the GUI produces the desired results, so the underlying data appear to be OK. [image]

Thanks very much for the code. I gave it a try, and I’m still getting the following message: “CalculateOutputGeometry: No image geometry specified, default geometry is calculated”. The output volume is still just an array of zeros as well. I’m not sure why this happens, and I’ve confirmed that the r…

Thanks for sharing the script that worked for you. Probably the very latest Slicer Preview Release (that you download today or later) would work with the shorter script I provided ( @Sam_Horvath pushed a fix for properly handling STL files in either RAS or LPS coordinate system).

Sorry for the slow reply. I downloaded the latest Slicer Preview Release (2020-09-01) to test the shorter script you provided and the code now works! The “CalculateOutputGeometry: No image geometry specified, default geometry is calculated” message still appears, but the resulting label maps are per…

Hi, Thank you for this thread. I am able to convert my Model ‘.stl’ files to Segmentations ‘.seg.nrrd’ files. I am not facing the direction related issue. But I wanted to know how to set the Segmentation labelmap geometry using python code, rather than using Segment Editor in GUI. My Code - refe…

See a complete example for specifying segmentation geometry in the script repository .

Hello sir, I don’t know if you have time, but I would like to ask you a question. After converting STL data to Nii.gz data, my own STL file was complete, but I found that many neural tubes were broken after conversion. I don’t know how to reduce this kind of breakage. Do you have a good solution

Hello friends, I have a folder containing STL masks of lesions from my dataset, and I want to extract Radiomics features. Should I first convert the STLs to binary masks? If it’s not necessary to convert them for feature extraction, please let me know how to extract features directly from STL files…

Converting .stl files to binary label maps in .nii format using Python

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Converting .stl files to binary label maps in .nii format using Python

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