Error when changing segment name from Python

Development
,
1

Hello 3D Slicer community,

I want to change (rename) segment names while using 3D Slicer. However, whenever I try to do this, I keep encountering errors or the segment names are not changing successfully. This has become quite problematic for me, as using the correct segment names is very important in my projects.

Below, I am sharing the code I am using. I would greatly appreciate it if you could review my code and help me with any errors or issues I am facing.

Any advice will be appreciated! Thanks!

import os
import slicer
import vtk

script_dir = os.path.dirname(os.path.realpath(_file_))
txt_path = os.path.join(script_dir, "..", "level", "Level5.txt")

def update_segment_names(outputFolder, txt_file_path=txt_path):
    subfolders = [f for f in os.listdir(outputFolder) if os.path.isdir(os.path.join(outputFolder, f))]

    for subfolder in subfolders:
        subfolder_path = os.path.join(outputFolder, subfolder)
        for f in os.listdir(subfolder_path):
            if f.endswith('.nii') and "_280" in f:
                nii_file_path = os.path.join(subfolder_path, f)

                
                slicer.mrmlScene.Clear(0)

               
                segmentation_node = slicer.util.loadSegmentation(nii_file_path)
                if not segmentation_node:
                    print(f"Segmentasyon dosyası {nii_file_path} yüklenemedi.")
                    continue

                
                segment_names = []
                try:
                    with open(txt_file_path, 'r') as file:
                        for line in file:
                            columns = line.strip().split()
                            if len(columns) >= 2:
                                segment_names.append(columns[1])
                except FileNotFoundError:
                    print(f"TXT dosyası {txt_file_path} bulunamadı.")
                    continue

                segmentation = segmentation_node.GetSegmentation()
                segment_ids = vtk.vtkStringArray()
                segmentation.GetSegmentIDs(segment_ids)

                
                for i in range(segment_ids.GetNumberOfValues()):
                    segment_id = segment_ids.GetValue(i)
                    segment = segmentation.GetSegment(segment_id)
                    old_name = segment.GetName()
                    if i < len(segment_names):
                        segment.SetName(segment_names[i])
                    else:
                        segment.SetName(f"Segment_{i}")

                    print(f"Eski isim: {old_name}, Yeni isim: {segment.GetName()}")

                
                labelmap_volume_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
                slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode(segmentation_node, labelmap_volume_node)

               
                volumesLogic = slicer.modules.volumes.logic()
                scalar_volume_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode")  
                scalar_volume_node.SetName(segmentation_node.GetName()) 
                volumesLogic.CreateScalarVolumeFromVolume(slicer.mrmlScene, labelmap_volume_node, scalar_volume_node)

               
                output_nifti_path = os.path.join(subfolder_path, f"{os.path.splitext(f)[0]}.nii")
                success = slicer.util.saveNode(labelmap_volume_node, output_nifti_path)

                if success:
                    print(f"Segmentasyon güncellendi ve kaydedildi: {output_nifti_path}")
                else:
                    print(f"Segmentasyon kaydedilemedi: {output_nifti_path}")

                
                slicer.mrmlScene.RemoveNode(segmentation_node)
                slicer.mrmlScene.RemoveNode(labelmap_volume_node)
                slicer.mrmlScene.RemoveNode(scalar_volume_node)
2

Hi! I think it would facilitate things if you shared a minimal code example that does not work for you. All the people who help out here are quite busy, so I think posting multi-page code discourages some of them. Thanks!