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

**URL:** <https://discourse.slicer.org/t/stl-file-stores-the-annotation-results-of-ct-data-and-i-want-to-convert-it-to-nii-format-for-deep-learning/27898>\
**Category:** Support\
**Tags:** segmentation, dicom, python, 3d-model\
**Created:** [February 18, 2023, 4:53am UTC](https://discourse.slicer.org/t/stl-file-stores-the-annotation-results-of-ct-data-and-i-want-to-convert-it-to-nii-format-for-deep-learning/27898 "2023-02-18T04:53:18Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![missile](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/missile/32/18447_2.png) [@missile](https://discourse.slicer.org/u/missile)\
**Post date:** [February 18, 2023, 4:53am UTC](https://discourse.slicer.org/t/stl-file-stores-the-annotation-results-of-ct-data-and-i-want-to-convert-it-to-nii-format-for-deep-learning/27898/1 "2023-02-18T04:53:19Z")

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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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<div class="post-metadata">

**Author:** ![missile](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/missile/32/18447_2.png) [@missile](https://discourse.slicer.org/u/missile)\
**Post date:** [February 17, 2023, 5:18pm UTC](https://discourse.slicer.org/t/stl-file-stores-the-annotation-results-of-ct-data-and-i-want-to-convert-it-to-nii-format-for-deep-learning/27898/2 "2023-02-17T17:18:19Z")

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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)