stl file stores the annotation results of CT data, and I want to convert it to nii format for deep learning.

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Operating system:Hii,
I am having trouble applying the module in slicer 5.0.2. My situation is the stl file stores the annotation results of CT data, and I want to convert it to nii format for deep learning.
When i press apply, it saysreferenceVolumeNode = slicer.util.loadVolume(reference_volume_path), which keeps giving me an error about not being able to load noad from file.2
Detailed error:
Traceback (most recent call last):
File “”, line 7, in
File “D:\Slicer 5.0.2\bin\Python\slicer\util.py”, line 908, in loadVolume
return loadNodeFromFile(filename, filetype, properties, returnNode)
File “D:\Slicer 5.0.2\bin\Python\slicer\util.py”, line 681, in loadNodeFromFile
raise RuntimeError(errorMessage)
RuntimeError: Failed to load node from file: D:\change\dicom\2.nii.gz

Below is my code

import os
import slicer
stl_path = r"D:\change\stl"
image_path = r"D:\change\dicom"
out_path = r"D:\change\nii"
patients = os.listdir(stl_path)
for patient in patients:
patient_path = os.path.join(stl_path, patient)
stl_files = os.listdir(patient_path)
output_file_path = os.path.join(out_path, patient)
os.makedirs(output_file_path, exist_ok=True)
reference_volume_path = os.path.join(image_path, patient+“.nii.gz”)
referenceVolumeNode = slicer.util.loadVolume(reference_volume_path)
for stl_file in stl_files:
stl_file_name = os.path.join(patient_path, stl_file)
output_file_name = os.path.join(output_file_path, stl_file[0:-4] + “.nii.gz”)
segmentationNode = slicer.util.loadSegmentation(stl_file_name)
outputLabelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass(‘vtkMRMLLabelMapVolumeNode’)
slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, outputLabelmapVolumeNode,
referenceVolumeNode)
slicer.util.saveNode(outputLabelmapVolumeNode, output_file_name)
slicer.mrmlScene.Clear(0)
Slicer version:
Expected behavior:
Actual behavior:

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2

Hello sir, I don’t know if you have time, but I would like to ask you a question.

My situation is the same as yours, the stl file stores the annotation results of CT data, and I want to convert it to nii format for deep learning. I reproduced the code from your post into the Python interactor in slicer, but I keep getting

referenceVolumeNode = slicer.util.loadVolume(reference_volume_path), which keeps giving me an error about not being able to load noad from file.

I’m very confused and I’m looking forward to your help when you have time.

Below is my code

import os
import slicer
stl_path = r"D:\change\stl"
image_path = r"D:\change\dicom"
out_path = r"D:\change\nii"
patients = os.listdir(stl_path)
for patient in patients:
patient_path = os.path.join(stl_path, patient)
stl_files = os.listdir(patient_path)
output_file_path = os.path.join(out_path, patient)
os.makedirs(output_file_path, exist_ok=True)
reference_volume_path = os.path.join(image_path, patient+“.nii.gz”)
referenceVolumeNode = slicer.util.loadVolume(reference_volume_path)
for stl_file in stl_files:
stl_file_name = os.path.join(patient_path, stl_file)
output_file_name = os.path.join(output_file_path, stl_file[0:-4] + “.nii.gz”)
segmentationNode = slicer.util.loadSegmentation(stl_file_name)
outputLabelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass(‘vtkMRMLLabelMapVolumeNode’)
slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, outputLabelmapVolumeNode,
referenceVolumeNode)
slicer.util.saveNode(outputLabelmapVolumeNode, output_file_name)
slicer.mrmlScene.Clear(0)

1 Like