# TotalSegmentator Partial Segmentation

**URL:** <https://discourse.slicer.org/t/totalsegmentator-partial-segmentation/47335>\
**Category:** Support\
**Tags:** totalsegmentator\
**Created:** [June 14, 2026, 7:44pm UTC](https://discourse.slicer.org/t/totalsegmentator-partial-segmentation/47335 "2026-06-14T19:44:32Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Arash1](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/arash1/32/78865_2.png) [@Arash1](https://discourse.slicer.org/u/Arash1)\
**Post date:** [June 14, 2026, 7:44pm UTC](https://discourse.slicer.org/t/totalsegmentator-partial-segmentation/47335/1 "2026-06-14T19:44:34Z")

</div>

Any suggestions on why the segment is like this?

 ![{17039586-98EB-4923-94DC-87DBE3160D26}](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/0/904d212d539ad565f7fe05cf1df82d911a930059.png)

[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - Session start time …: 20260614\_133634  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - Slicer version …: 5.10.0 (revision 34045 / a2b6d08) win-amd64 - installed release  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - Operating system …: Windows / Personal / (Build 26200, Code Page 65001) - 64-bit  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - Memory …: 63232 MB physical, 72448 MB virtual  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - CPU …: AuthenticAMD AMD Ryzen 9 8945HS w/ Radeon 780M Graphics, 16 cores, 16 logical processors  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - Qt configuration …: version 5.15.2, with SSL, requested OpenGL 3.2 (core profile)  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - DCMTK configuration …: version 3.6.8, no SSL  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - Internationalization …: enabled, language=  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - Developer mode …: disabled  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - Application path …: D:/3DSlicer510/bin  
[DEBUG][Qt] 14.06.2026 13:36:34 (unknown:0) - Additional module paths ..: [slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules](http://slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules), [slicer.org/Extensions-34045/NNUNet/lib/Slicer-5.10/qt-scripted-modules](http://slicer.org/Extensions-34045/NNUNet/lib/Slicer-5.10/qt-scripted-modules), [slicer.org/Extensions-34045/SlicerPythonTestRunner/lib/Slicer-5.10/qt-scripted-modules](http://slicer.org/Extensions-34045/SlicerPythonTestRunner/lib/Slicer-5.10/qt-scripted-modules), [slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules](http://slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules)  
[INFO][Stream] 14.06.2026 13:36:35 (unknown:0) -  
[WARNING][Python] 14.06.2026 13:36:36 [Python] (D:\3DSlicer510\lib\Python\Lib\site-packages\pydicom\misc.py:82) - get\_frame\_offsets is deprecated and will be removed in v4.0  
[DEBUG][Python] 14.06.2026 13:36:37 [Python] (D:\3DSlicer510\lib\Slicer-5.10\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentEditor  
[DEBUG][Python] 14.06.2026 13:36:37 [Python] (D:\3DSlicer510\lib\Slicer-5.10\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentStatistics  
[DEBUG][Qt] 14.06.2026 13:36:37 (unknown:0) - Switch to module: “Welcome”  
[DEBUG][Qt] 14.06.2026 13:36:40 (unknown:0) - Switch to module: “DICOM”  
[INFO][Python] 14.06.2026 13:36:52 [Python] (D:/3DSlicer510/bin/../lib/Slicer-5.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:445) - Loading with imageIOName: GDCM  
[WARNING][ITK] 14.06.2026 13:36:54 (unknown:0) - WARNING: In C:\D\S\S-0-build\ITK\Modules\IO\ImageBase\include\itkImageSeriesReader.hxx, line 478  
ImageSeriesReader (0000024CD4A2FDB0): Non uniform sampling or missing slices detected, maximum nonuniformity:0.000250045  
[DEBUG][Python] 14.06.2026 13:36:55 [Python] (D:/3DSlicer510/bin/../lib/Slicer-5.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:567) - DICOM window/level (40.0/300.0) set to volume ‘204: CT SOFT\_512x512 90min’ from SOP instance 1.3.6.1.4.1.14519.5.2.1.319576169887040151064629310950896265349.  
[DEBUG][Python] 14.06.2026 13:36:55 [Python] (D:/3DSlicer510/bin/../lib/Slicer-5.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:944) - Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 0.000143692 mm, tolerance threshold is 0.001 mm).  
[DEBUG][Qt] 14.06.2026 13:36:58 (unknown:0) - Switch to module: “CropVolume”  
[INFO][VTK] 14.06.2026 13:37:29 [vtkSlicerCLIModuleLogic (0000024CC171A100)] (C:\D\S\S-0\Base\Logic\vtkSlicerCLIModuleLogic.cxx:844) - Found CommandLine Module, target is D:/3DSlicer510/bin/../lib/Slicer-5.10/cli-modules/ResampleScalarVectorDWIVolume.exe  
[INFO][VTK] 14.06.2026 13:37:29 [vtkSlicerCLIModuleLogic (0000024CC171A100)] (C:\D\S\S-0\Base\Logic\vtkSlicerCLIModuleLogic.cxx:862) - ModuleType: CommandLineModule  
[INFO][VTK] 14.06.2026 13:37:29 [vtkSlicerCLIModuleLogic (0000024CC171A100)] (C:\D\S\S-0\Base\Logic\vtkSlicerCLIModuleLogic.cxx:1690) - Resample Scalar/Vector/DWI Volume command line:

D:/3DSlicer510/bin/../lib/Slicer-5.10/cli-modules/ResampleScalarVectorDWIVolume.exe --hfieldtype h-Field --interpolation linear --transform\_order output-to-input --image\_center input --spacing 0.48828125,0.48828125,0.48828125 --size 524,639,725 --origin 115.779,154.273,2003.54 --direction\_matrix -1,0,0,0,-1,0,0,0,1 --number\_of\_thread 0 --default\_pixel\_value 0 --window\_function c --spline\_order 3 --transform\_matrix 1,0,0,0,1,0,0,0,1,0,0,0 --transform a C:/Users/amanl/AppData/Local/Temp/Slicer/BFAGI\_vtkMRMLScalarVolumeNodeB.nrrd C:/Users/amanl/AppData/Local/Temp/Slicer/BFAGI\_vtkMRMLScalarVolumeNodeC.nrrd  
[INFO][VTK] 14.06.2026 13:37:32 [vtkSlicerCLIModuleLogic (0000024CC171A100)] (C:\D\S\S-0\Base\Logic\vtkSlicerCLIModuleLogic.cxx:1894) - Resample Scalar/Vector/DWI Volume completed without errors  
[DEBUG][Qt] 14.06.2026 13:37:38 (unknown:0) - Switch to module: “TotalSegmentator”  
[INFO][Python] 14.06.2026 13:37:56 [Python] (D:\3DSlicer510\lib\Python\Lib\site-packages\numexpr\utils.py:164) - NumExpr defaulting to 16 threads.  
[INFO][Python] 14.06.2026 13:38:24 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules/PyTorchUtils.py:153) - Importing torch…  
[INFO][Python] 14.06.2026 13:38:26 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules/PyTorchUtils.py:190) - PyTorch 2.12.0+cu126 imported successfully  
[INFO][Python] 14.06.2026 13:38:26 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules/PyTorchUtils.py:191) - CUDA available: True  
[INFO][Python] 14.06.2026 13:38:26 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Processing started  
[INFO][Python] 14.06.2026 13:38:26 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Writing input file to C:/Users/amanl/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-06-14\_13+38+26.322/total-segmentator-input.nii  
[INFO][Python] 14.06.2026 13:38:26 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Creating segmentations with TotalSegmentator AI…  
[INFO][Python] 14.06.2026 13:38:26 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Total Segmentator arguments: [‘-i’, ‘C:/Users/amanl/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-06-14\_13+38+26.322/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/amanl/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-06-14\_13+38+26.322/segmentation’, ‘–device’, ‘gpu’, ‘–ml’, ‘–task’, ‘craniofacial\_structures’, ‘–robust\_crop’, ‘–higher\_order\_resampling’]  
[INFO][Python] 14.06.2026 13:38:48 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) -  
[INFO][Python] 14.06.2026 13:38:49 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 0%| | 0/2 [00:00\<?, ?it/s]  
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[INFO][Python] 14.06.2026 13:39:35 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 37%|###7 | 93/250 [00:08\<00:12, 12.14it/s]  
[INFO][Python] 14.06.2026 13:39:35 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 38%|###8 | 95/250 [00:08\<00:12, 12.33it/s]  
[INFO][Python] 14.06.2026 13:39:35 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 39%|###8 | 97/250 [00:08\<00:12, 12.16it/s]  
[INFO][Python] 14.06.2026 13:39:36 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 40%|###9 | 99/250 [00:09\<00:12, 12.25it/s]  
[INFO][Python] 14.06.2026 13:39:36 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 40%|#### | 101/250 [00:09\<00:12, 12.40it/s]  
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[INFO][Python] 14.06.2026 13:39:36 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 42%|####2 | 105/250 [00:09\<00:11, 12.36it/s]  
[INFO][Python] 14.06.2026 13:39:36 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 43%|####2 | 107/250 [00:09\<00:11, 12.16it/s]  
[INFO][Python] 14.06.2026 13:39:36 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 44%|####3 | 109/250 [00:09\<00:11, 12.33it/s]  
[INFO][Python] 14.06.2026 13:39:37 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 44%|####4 | 111/250 [00:10\<00:11, 12.16it/s]  
[INFO][Python] 14.06.2026 13:39:37 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 45%|####5 | 113/250 [00:10\<00:11, 12.36it/s]  
[INFO][Python] 14.06.2026 13:39:37 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 46%|####6 | 115/250 [00:10\<00:11, 12.14it/s]  
[INFO][Python] 14.06.2026 13:39:37 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 47%|####6 | 117/250 [00:10\<00:10, 12.31it/s]  
[INFO][Python] 14.06.2026 13:39:37 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 48%|####7 | 119/250 [00:10\<00:10, 12.16it/s]  
[INFO][Python] 14.06.2026 13:39:37 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 48%|####8 | 121/250 [00:10\<00:10, 12.29it/s]  
[INFO][Python] 14.06.2026 13:39:38 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 49%|####9 | 123/250 [00:11\<00:10, 12.37it/s]  
[INFO][Python] 14.06.2026 13:39:38 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 50%|##### | 125/250 [00:11\<00:10, 12.17it/s]  
[INFO][Python] 14.06.2026 13:39:38 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 51%|##### | 127/250 [00:11\<00:10, 12.29it/s]  
[INFO][Python] 14.06.2026 13:39:38 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 52%|#####1 | 129/250 [00:11\<00:10, 12.08it/s]  
[INFO][Python] 14.06.2026 13:39:38 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 52%|#####2 | 131/250 [00:11\<00:09, 12.20it/s]  
[INFO][Python] 14.06.2026 13:39:38 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 53%|#####3 | 133/250 [00:11\<00:09, 12.29it/s]  
[INFO][Python] 14.06.2026 13:39:39 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 54%|#####4 | 135/250 [00:12\<00:09, 12.36it/s]  
[INFO][Python] 14.06.2026 13:39:39 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 55%|#####4 | 137/250 [00:12\<00:09, 12.18it/s]  
[INFO][Python] 14.06.2026 13:39:39 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 56%|#####5 | 139/250 [00:12\<00:09, 12.10it/s]  
[INFO][Python] 14.06.2026 13:39:39 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 56%|#####6 | 141/250 [00:12\<00:08, 12.23it/s]  
[INFO][Python] 14.06.2026 13:39:39 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 57%|#####7 | 143/250 [00:12\<00:08, 12.39it/s]  
[INFO][Python] 14.06.2026 13:39:39 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 58%|#####8 | 145/250 [00:12\<00:08, 12.11it/s]  
[INFO][Python] 14.06.2026 13:39:40 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 59%|#####8 | 147/250 [00:13\<00:08, 12.05it/s]  
[INFO][Python] 14.06.2026 13:39:40 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 60%|#####9 | 149/250 [00:13\<00:08, 12.18it/s]  
[INFO][Python] 14.06.2026 13:39:40 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 60%|###### | 151/250 [00:13\<00:08, 12.32it/s]  
[INFO][Python] 14.06.2026 13:39:40 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 61%|######1 | 153/250 [00:13\<00:08, 12.11it/s]  
[INFO][Python] 14.06.2026 13:39:40 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 62%|######2 | 155/250 [00:13\<00:07, 12.25it/s]  
[INFO][Python] 14.06.2026 13:39:40 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 63%|######2 | 157/250 [00:13\<00:07, 12.42it/s]  
[INFO][Python] 14.06.2026 13:39:41 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 64%|######3 | 159/250 [00:14\<00:07, 12.26it/s]  
[INFO][Python] 14.06.2026 13:39:41 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 64%|######4 | 161/250 [00:14\<00:07, 12.15it/s]  
[INFO][Python] 14.06.2026 13:39:41 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 65%|######5 | 163/250 [00:14\<00:07, 12.26it/s]  
[INFO][Python] 14.06.2026 13:39:41 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 66%|######6 | 165/250 [00:14\<00:07, 12.14it/s]  
[INFO][Python] 14.06.2026 13:39:41 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 67%|######6 | 167/250 [00:14\<00:06, 12.27it/s]  
[INFO][Python] 14.06.2026 13:39:41 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 68%|######7 | 169/250 [00:14\<00:06, 12.41it/s]  
[INFO][Python] 14.06.2026 13:39:42 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 68%|######8 | 171/250 [00:14\<00:06, 12.19it/s]  
[INFO][Python] 14.06.2026 13:39:42 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 69%|######9 | 173/250 [00:15\<00:06, 12.32it/s]  
[INFO][Python] 14.06.2026 13:39:42 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 70%|####### | 175/250 [00:15\<00:06, 12.11it/s]  
[INFO][Python] 14.06.2026 13:39:42 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 71%|####### | 177/250 [00:15\<00:05, 12.26it/s]  
[INFO][Python] 14.06.2026 13:39:42 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 72%|#######1 | 179/250 [00:15\<00:05, 12.39it/s]  
[INFO][Python] 14.06.2026 13:39:42 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 72%|#######2 | 181/250 [00:15\<00:05, 12.19it/s]  
[INFO][Python] 14.06.2026 13:39:43 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 73%|#######3 | 183/250 [00:15\<00:05, 12.34it/s]  
[INFO][Python] 14.06.2026 13:39:43 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 74%|#######4 | 185/250 [00:16\<00:05, 12.07it/s]  
[INFO][Python] 14.06.2026 13:39:43 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 75%|#######4 | 187/250 [00:16\<00:05, 12.34it/s]  
[INFO][Python] 14.06.2026 13:39:43 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 76%|#######5 | 189/250 [00:16\<00:05, 12.10it/s]  
[INFO][Python] 14.06.2026 13:39:43 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 76%|#######6 | 191/250 [00:16\<00:04, 12.29it/s]  
[INFO][Python] 14.06.2026 13:39:43 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 77%|#######7 | 193/250 [00:16\<00:04, 12.08it/s]  
[INFO][Python] 14.06.2026 13:39:43 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 78%|#######8 | 195/250 [00:16\<00:04, 12.30it/s]  
[INFO][Python] 14.06.2026 13:39:44 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 79%|#######8 | 197/250 [00:17\<00:04, 12.11it/s]  
[INFO][Python] 14.06.2026 13:39:44 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 80%|#######9 | 199/250 [00:17\<00:04, 12.27it/s]  
[INFO][Python] 14.06.2026 13:39:44 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 80%|######## | 201/250 [00:17\<00:04, 12.13it/s]  
[INFO][Python] 14.06.2026 13:39:44 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 81%|########1 | 203/250 [00:17\<00:03, 12.27it/s]  
[INFO][Python] 14.06.2026 13:39:44 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 82%|########2 | 205/250 [00:17\<00:03, 12.15it/s]  
[INFO][Python] 14.06.2026 13:39:44 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 83%|########2 | 207/250 [00:17\<00:03, 12.31it/s]  
[INFO][Python] 14.06.2026 13:39:45 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 84%|########3 | 209/250 [00:18\<00:03, 12.41it/s]  
[INFO][Python] 14.06.2026 13:39:45 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 84%|########4 | 211/250 [00:18\<00:03, 12.15it/s]  
[INFO][Python] 14.06.2026 13:39:45 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 85%|########5 | 213/250 [00:18\<00:03, 12.33it/s]  
[INFO][Python] 14.06.2026 13:39:45 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 86%|########6 | 215/250 [00:18\<00:02, 12.11it/s]  
[INFO][Python] 14.06.2026 13:39:45 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 87%|########6 | 217/250 [00:18\<00:02, 12.27it/s]  
[INFO][Python] 14.06.2026 13:39:45 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 88%|########7 | 219/250 [00:18\<00:02, 12.14it/s]  
[INFO][Python] 14.06.2026 13:39:46 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 88%|########8 | 221/250 [00:19\<00:02, 12.25it/s]  
[INFO][Python] 14.06.2026 13:39:46 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 89%|########9 | 223/250 [00:19\<00:02, 12.44it/s]  
[INFO][Python] 14.06.2026 13:39:46 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 90%|######### | 225/250 [00:19\<00:02, 12.24it/s]  
[INFO][Python] 14.06.2026 13:39:46 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 91%|######### | 227/250 [00:19\<00:01, 12.35it/s]  
[INFO][Python] 14.06.2026 13:39:46 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 92%|#########1| 229/250 [00:19\<00:01, 12.18it/s]  
[INFO][Python] 14.06.2026 13:39:46 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 92%|#########2| 231/250 [00:19\<00:01, 12.30it/s]  
[INFO][Python] 14.06.2026 13:39:47 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 93%|#########3| 233/250 [00:20\<00:01, 12.17it/s]  
[INFO][Python] 14.06.2026 13:39:47 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 94%|#########3| 235/250 [00:20\<00:01, 12.35it/s]  
[INFO][Python] 14.06.2026 13:39:47 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 95%|#########4| 237/250 [00:20\<00:01, 12.12it/s]  
[INFO][Python] 14.06.2026 13:39:47 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 96%|#########5| 239/250 [00:20\<00:00, 12.36it/s]  
[INFO][Python] 14.06.2026 13:39:47 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 96%|#########6| 241/250 [00:20\<00:00, 12.16it/s]  
[INFO][Python] 14.06.2026 13:39:47 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 97%|#########7| 243/250 [00:20\<00:00, 12.35it/s]  
[INFO][Python] 14.06.2026 13:39:48 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 98%|#########8| 245/250 [00:21\<00:00, 12.09it/s]  
[INFO][Python] 14.06.2026 13:39:48 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 99%|#########8| 247/250 [00:21\<00:00, 12.32it/s]  
[INFO][Python] 14.06.2026 13:39:48 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 100%|#########9| 249/250 [00:21\<00:00, 12.14it/s]  
[INFO][Python] 14.06.2026 13:39:48 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - 100%|##########| 250/250 [00:21\<00:00, 11.66it/s]  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) -  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - If you use this tool please cite: [https://pubs.rsna.org/doi/10.1148/ryai.230024](https://pubs.rsna.org/doi/10.1148/ryai.230024)  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) -  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Generating rough segmentation for cropping…  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - (Using more robust (but slower) 3mm model for cropping.)  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Resampling…  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Resampled in 5.34s  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Predicting…  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Predicted in 14.52s  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Resampling…  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - cropping from (524, 639, 725) to (372, 476, 581)  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Resampling…  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Resampled in 16.81s  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Predicting…  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Predicted in 39.11s  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Resampling…  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Saving segmentations…  
[INFO][Python] 14.06.2026 13:40:19 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Saved in 2.69s  
[INFO][Python] 14.06.2026 13:40:20 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Importing segmentation results…  
[INFO][VTK] 14.06.2026 13:40:20 [vtkMRMLSegmentationStorageNode (0000024D79349490)] (C:\D\S\S-0\Libs\MRML\Core\vtkMRMLSegmentationStorageNode.cxx:608) - ReferenceImageExtentOffset attribute was not found in NRRD segmentation file. Assume no offset.  
[INFO][Python] 14.06.2026 13:40:21 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Processing completed in 114.95 seconds  
[INFO][Python] 14.06.2026 13:40:21 [Python] (D:/3DSlicer510/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:690) - Cleaning up temporary folder…

---

<div class="post-metadata">

**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [June 14, 2026, 10:30pm UTC](https://discourse.slicer.org/t/totalsegmentator-partial-segmentation/47335/2 "2026-06-14T22:30:41Z")

</div>

Try executing TotalSegmentator with a test dataset and let us know how it goes? Also, see if you get different behavior by using other models (e.g. ‘total’ or ‘total\_mr’)

---

<div class="post-metadata">

**Author:** ![Arash1](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/arash1/32/78865_2.png) [@Arash1](https://discourse.slicer.org/u/Arash1)\
**Post date:** [June 15, 2026, 3:56am UTC](https://discourse.slicer.org/t/totalsegmentator-partial-segmentation/47335/3 "2026-06-15T03:56:00Z")

</div>

The test model is fine.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/0/509bcd58979e0659c90d96c6b67623c3673e581e.jpeg)

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/6/46fe093d4c5109f5acee2609b591ba0dcade0b2f.jpeg)

---

<div class="post-metadata">

**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [June 15, 2026, 2:46pm UTC](https://discourse.slicer.org/t/totalsegmentator-partial-segmentation/47335/4 "2026-06-15T14:46:54Z")

</div>

Then the problem is probably your dataset

I’d guess this is part of the problem:

> [INFO][Python] 14.06.2026 13:36:52 [Python] (D:/3DSlicer510/bin/../lib/Slicer-5.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:445) - Loading with imageIOName: GDCM  
> [WARNING][ITK] 14.06.2026 13:36:54 (unknown:0) - WARNING: In C:\D\S\S-0-build\ITK\Modules\IO\ImageBase\include\itkImageSeriesReader.hxx, line 478  
> ImageSeriesReader (0000024CD4A2FDB0): **Non uniform sampling or missing slices detected** , maximum nonuniformity:0.000250045