TotalSegmentator Issues

[arflores]

Hello,

I am new to TotalSegmentator. I am trying to use it to autosegment vertebral bodies on CTs.

I am using an iMac with Radeon Pro 5500 XT 8GB GDDR6 memory (not sure if this is compatible/usable?). I am using Slicer 5.6.2 and the most recent stable TotalSegmentator (as of today). For input, I select the CT I’ve uploaded. I choose vertebra body as task. I’ve tried both “fast” and full resolution options and get the same error (below). Of note, it indicates “no GPU detected” so I think it is using CPU only. I also tried the totalsegmentator.com and this gave Internal server error. Anyway, the error I get in Slicer:

Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/bin/Python/slicer/util.py”, line 3255, in tryWithErrorDisplay
yield
File “/Applications/Slicer.app/Contents/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py”, line 298, in onApplyButton
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
File “/Applications/Slicer.app/Contents/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py”, line 971, in process
self.processVolume(inputFile, inputVolume,
File “/Applications/Slicer.app/Contents/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py”, line 1045, in processVolume
self.logProcessOutput(proc)
File “/Applications/Slicer.app/Contents/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py”, line 817, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[’/Applications/Slicer.app/Contents/bin/…/bin/PythonSlicer’, ‘/Applications/Slicer.app/Contents/lib/Python/bin/TotalSegmentator’, ‘-i’, ‘/private/var/folders/7q/zlc8w0qx549dl50655_1s_7m0000gn/T/Slicer-alexflores/__SlicerTemp__2024-07-31_09+30+29.195/total-segmentator-input.nii’, ‘-o’, ‘/private/var/folders/7q/zlc8w0qx549dl50655_1s_7m0000gn/T/Slicer-alexflores/__SlicerTemp__2024-07-31_09+30+29.195/segmentation’, ‘–task’, ‘vertebrae_body’]’ returned non-zero exit status 1.

Any help on this?

Thanks
Alex

[Matteboo]

Thank you for this very precise error report.

Have you tried to run total segmentator on the sample CT that are already available in slicer ?
Also, how much free space do you have on your disk? Sometimes, on my computer, if
i have little space left (>10Go) it causes issues

[diazandr3s (Andres Diaz-Pinto)]

Hi @arflores,

Have you considered using Auto3DSeg on Slicer?

New extension: MONAI Auto3DSeg - raise the bar in AI medical image segmentation

New extension: MONAI Auto3DSeg - raise the bar in AI medical image segmentation MONAI Auto3DSeg extension is a collaboration between MONAI and 3D Slicer developer teams (led by Andres Diaz Pinto - NVIDIA and Andras Lasso - PerkLab) to improve on the state-of-the-art in fully automatic 3D medical image segmentation and make the results widely accessible. The extension comes with dozens of pre-trained segmentation models for specific clinical use cases, which are designed to be fast and run anywh…

Just downloaded the latest Slicer and then install Auto3DSeg using Extension Manager. We made several models available (full res and quick) incuding Spine segmentation.

Hope this helps,