In line with this error, i get a similar one and don’t know why: Traceback (most recent call last): File “C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\bin\Python\slicer\util.py”, line 2961, in tryWithErrorDisplay yield File “C:/Users/Augusto/AppData/Local/NA-MIC/Slicer 5.2.1/NA-MIC/Extensions-31317/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py”, line 258, in onApplyButton self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(), File “C:/Users/Augusto/AppData/Local/NA-MIC/Slicer 5.2.1/NA-MIC/Extensions-31317/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py”, line 716, in process self.logProcessOutput(proc) File “C:/Users/Augusto/AppData/Local/NA-MIC/Slicer 5.2.1/NA-MIC/Extensions-31317/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py”, line 625, in logProcessOutput raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr) subprocess.CalledProcessError: Command ‘[‘C:/Users/Augusto/AppData/Local/NA-MIC/Slicer 5.2.1/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\Augusto\AppData\Local\NA-MIC\Slicer 5.2.1\lib\Python\Scripts\TotalSegmentator’, ‘-i’, ‘C:/Users/Augusto/AppData/Local/Temp/Slicer/__SlicerTemp__2022-12-15_14+38+59.132/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/Augusto/AppData/Local/Temp/Slicer/__SlicerTemp__2022-12-15_14+38+59.132/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 120. Anyone can help?

Hi all, I have just tried the extension in fast mode (because no GPU is detected) and it gives me a similar error: Traceback (most recent call last): File “/Applications/Slicer.app/Contents/bin/Python/slicer/util.py”, line 2961, in tryWithErrorDisplay yield File “/Applications/Slicer.app/Contents/Extensions-31317/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py”, line 258, in onApplyButton self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(), File “/Applications/Slicer.app/Contents/Extensions-31317/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py”, line 715, in process self.logProcessOutput(proc) File “/Applications/Slicer.app/Contents/Extensions-31317/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py”, line 624, 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/yg/g0dyz18s69dcy2q5jm2tgf340000gn/T/Slicer-francesco/__SlicerTemp__2022-12-17_15+59+32.173/total-segmentator-input.nii’, ‘-o’, ‘/private/var/folders/yg/g0dyz18s69dcy2q5jm2tgf340000gn/T/Slicer-francesco/__SlicerTemp__2022-12-17_15+59+32.173/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 1. I have already tried the workarounds suggested in previous posts, including the terminal command “%localappdata%\NA-MIC\Slicer 5.2.1\bin\PythonSlicer.EXE” -m pip install torch torchvision torchaudio --force-reinstall" and the command “%localappdata%\na-mic\Slicer 5.2.1\bin\PythonSlicer.exe” -m pip install git+https://github.com/wasserth/TotalSegmentator.git --no-deps. However, I always get the error. I am working with Slicer 5.2.1 on macOS 11.4. Thank you very much for the support!

[image] FraRizzetto: I have already tried the workarounds suggested in previous posts Those commands were not all for fixing issues but for diagnosing issues. If you executed those then they may have messed up your environment. For figuring out what’s wrong on your system, please remove Slicer, reinstall from scratch, run the segmentation on a Slicer sample data set, and provide here the content of the textbox under the Apply button.

I removed Slicer, reinstalled it and the TotalSegmentator extension, and tried it (fast mode) on a Slicer sample data. This time it asked me for updating PyTorch, then it ran smoothly performing the segmentations. Simple but effective advice. Thanks a lot!

may the weights pre-downloaded by googledrive or somewhere else. Use this plugin downing weights would be terriable for me .cause I can’t download the weights file because of some ssl or network error.

Have you really tried it yet? What were the configuration, data, machine, and network, what did you expect to happen, and what did not work? Can you provide a log from the TotalSegmentator extension output textbox? Please avoid posting the same problem in different threads. Thank you.

Sorry for submitting duplicate questions many times. here is the logs Downloading pretrained weights for Task 251 (~230MB) ... Traceback (most recent call last): File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\urllib3\connection.py", line 159, in _new_conn conn = connection.create_connection( File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\urllib3\util\connection.py", line 61, in create_connection for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM): File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\socket.py", line 954, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): socket.gaierror: [Errno 11004] getaddrinfo failed During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\urllib3\connectionpool.py", line 670, in urlopen httplib_response = self._make_request( File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\urllib3\connectionpool.py", line 381, in _make_request self._validate_conn(conn) File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\urllib3\connectionpool.py", line 978, in _validate_conn conn.connect() File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\urllib3\connection.py", line 309, in connect conn = self._new_conn() File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\urllib3\connection.py", line 171, in _new_conn raise NewConnectionError( urllib3.exceptions.NewConnectionError: : Failed to establish a new connection: [Errno 11004] getaddrinfo failed During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\requests\adapters.py", line 489, in send resp = conn.urlopen( File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\urllib3\connectionpool.py", line 726, in urlopen retries = retries.increment( File "C:\Users\someone\AppData\Local\NA-MIC\Slicer 5.3.0-2023-01-13\lib\Python\Lib\site-packages\urllib3\util\retry.py", line 446, in increment raise MaxRetryError(_pool, url, error or ResponseError(cause)) urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='zenodo.org', port=443): Max retries exceeded with url: /record/6802342/files/Task251_TotalSegmentator_part1_organs_1139subj.zip?download=1 (Caused by NewConnectionError(' : Failed to establish a new connection: [Errno 11004] getaddrinfo failed'))

Sorry for submitting duplicate questions many times again the questions are following: can I load weights manually, without using slicer to download weights in case of bad network situation can I use my own trained weight and model to infer the segmentation with your code framework thank you

Thanks for the details. Please allow some time for checking this out with the developer of TotalSegmentator and on our own systems.

Just tested this with a fresh 3D Slicer 5.3.0. PyTorch and TotalSegmentator installed fine with no problems. Please understand that the TotalSegmentator extension wraps the program for ease of use in 3D Slicer, and the original code is maintained here. Your problem indicates a maybe regional network issue during access to Zenodo and similar problems have already been reported in the TotalSegmentator issue tracker on GitHub. Please try installing Slicer and TS on a different machine or in a different network.

You can download the weights manually and put them in the folder where 3D Slicer needs them. @lassoan can tell you where the weights are stored for the TotalSegmentator 3D Slicer extension. The links to the weights can be seen here: wasserth/TotalSegmentator/blob/master/totalsegmentator/libs.py#L75 with zipfile.ZipFile(config_dir / "tmp_download_file.zip", 'r') as zip_f: zip_f.extractall(config_dir) print(f" downloaded in {time.time()-st:.2f}s") except Exception as e: raise e finally: if tempfile.exists(): os.remove(tempfile) def download_pretrained_weights(task_id): if "TOTALSEG_WEIGHTS_PATH" in os.environ: config_dir = Path(os.environ["TOTALSEG_WEIGHTS_PATH"]) / "nnUNet" else: # in docker container finding home not properly working therefore map to /tmp home_path = Path("/tmp") if str(Path.home()) == "/" else Path.home() config_dir = home_path / ".totalsegmentator/nnunet/results/nnUNet" (config_dir / "3d_fullres").mkdir(exist_ok=True, parents=True) (config_dir / "2d").mkdir(exist_ok=True, parents=True) You could also replace those weights by your own trained weights. But you might easily run into problems doing this. You should be familiar with python when you do this.

TotalSegmentator error at first run: Command ...Python\Scripts\TotalSegmentator... returned non-zero exit status 120

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TotalSegmentator error at first run: Command ...Python\Scripts\TotalSegmentator... returned non-zero exit status 120

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