TotalSegmentator error at first run: "Command ‘pip’, ‘install’, ‘git+https://github.com/wasserth/TotalSegmentator.git’, ‘–no-deps’]’ returned non-zero exit status"

Support
41

Thank you for your reply!
When i try with Slicer 5.3.0,there is new error.How can I solve this problem?thx！
Here are the error infos。

Traceback (most recent call last):

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\bin\Python\slicer\util.py”, line 2973, in tryWithErrorDisplay

yield

File “C:/Users/sain/Desktop/3DSilcer/Slicer 5.3.0/slicer.org/Extensions-31734/TotalSegmentator/lib/Slicer-5.3/qt-scripted-modules/TotalSegmentator.py”, line 264, in onApplyButton

self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),

File “C:/Users/sain/Desktop/3DSilcer/Slicer 5.3.0/slicer.org/Extensions-31734/TotalSegmentator/lib/Slicer-5.3/qt-scripted-modules/TotalSegmentator.py”, line 799, in process

self.logProcessOutput(proc)

File “C:/Users/sain/Desktop/3DSilcer/Slicer 5.3.0/slicer.org/Extensions-31734/TotalSegmentator/lib/Slicer-5.3/qt-scripted-modules/TotalSegmentator.py”, line 692, in logProcessOutput

raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)

subprocess.CalledProcessError: Command ‘[‘C:/Users/sain/Desktop/3DSilcer/Slicer 5.3.0/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Scripts\TotalSegmentator’, ‘-i’, ‘C:/Users/sain/AppData/Local/Temp/Slicer/__SlicerTemp__2023-05-10_09+14+18.597/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/sain/AppData/Local/Temp/Slicer/__SlicerTemp__2023-05-10_09+14+18.597/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 1.

42

What is the pytorch and NVIDIA driver version displayed in Pytorch Utils module?

Could you try to run the segmentation again and copy here all the output that you can find the the application log (menu: Help / Report a bug)?

43

PyTorch:installed version 2.0.1+cu118
NVIDIA driver:installed version 531.14

I try to run the segmentation again and here are all the output。

Processing started

Writing input file to C:/Users/sain/AppData/Local/Temp/Slicer/__SlicerTemp__2023-05-10_10+01+57.716/total-segmentator-input.nii

Creating segmentations with TotalSegmentator AI…

Total Segmentator arguments: [‘-i’, ‘C:/Users/sain/AppData/Local/Temp/Slicer/__SlicerTemp__2023-05-10_10+01+57.716/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/sain/AppData/Local/Temp/Slicer/__SlicerTemp__2023-05-10_10+01+57.716/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]

If you use this tool please cite: [2208.05868] TotalSegmentator: robust segmentation of 104 anatomical structures in CT images

Using ‘fast’ option: resampling to lower resolution (3mm)

Downloading pretrained weights for Task 256 (~230MB) …

Traceback (most recent call last):

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\urllib3\connection.py”, line 174, in _new_conn

conn = connection.create_connection(

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\urllib3\util\connection.py”, line 72, in create_connection

for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\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\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 703, in urlopen

httplib_response = self._make_request(

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 386, in _make_request

self._validate_conn(conn)

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 1042, in _validate_conn

conn.connect()

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\urllib3\connection.py”, line 358, in connect

self.sock = conn = self._new_conn()

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\urllib3\connection.py”, line 186, in _new_conn

raise NewConnectionError(

urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x000002D3ADC85D90>: 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\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\requests\adapters.py”, line 489, in send

resp = conn.urlopen(

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 787, in urlopen

retries = retries.increment(

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\urllib3\util\retry.py”, line 592, 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/6802052/files/Task256_TotalSegmentator_3mm_1139subj.zip?download=1 (Caused by NewConnectionError(‘<urllib3.connection.HTTPSConnection object at 0x000002D3ADC85D90>: 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\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Scripts\TotalSegmentator”, line 93, in

main()

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Scripts\TotalSegmentator”, line 86, in main

totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\totalsegmentator\python_api.py”, line 157, in totalsegmentator

download_pretrained_weights(task_id)

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\totalsegmentator\libs.py”, line 183, in download_pretrained_weights

download_url_and_unpack(WEIGHTS_URL, config_dir)

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\totalsegmentator\libs.py”, line 69, in download_url_and_unpack

raise e

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\totalsegmentator\libs.py”, line 55, in download_url_and_unpack

with requests.get(url, stream=True) as r:

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\requests\api.py”, line 73, in get

return request(“get”, url, params=params, **kwargs)

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\requests\api.py”, line 59, in request

return session.request(method=method, url=url, **kwargs)

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\requests\sessions.py”, line 587, in request

resp = self.send(prep, **send_kwargs)

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\requests\sessions.py”, line 701, in send

r = adapter.send(request, **kwargs)

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Lib\site-packages\requests\adapters.py”, line 565, in send

raise ConnectionError(e, request=request)

requests.exceptions.ConnectionError: HTTPSConnectionPool(host=‘zenodo.org’, port=443): Max retries exceeded with url: /record/6802052/files/Task256_TotalSegmentator_3mm_1139subj.zip?download=1 (Caused by NewConnectionError(‘<urllib3.connection.HTTPSConnection object at 0x000002D3ADC85D90>: Failed to establish a new connection: [Errno 11004] getaddrinfo failed’))

Failed to compute results.

Command ‘[‘C:/Users/sain/Desktop/3DSilcer/Slicer 5.3.0/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Scripts\TotalSegmentator’, ‘-i’, ‘C:/Users/sain/AppData/Local/Temp/Slicer/__SlicerTemp__2023-05-10_10+01+57.716/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/sain/AppData/Local/Temp/Slicer/__SlicerTemp__2023-05-10_10+01+57.716/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 1.

Traceback (most recent call last):

File “C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\bin\Python\slicer\util.py”, line 2973, in tryWithErrorDisplay

yield

File “C:/Users/sain/Desktop/3DSilcer/Slicer 5.3.0/slicer.org/Extensions-31734/TotalSegmentator/lib/Slicer-5.3/qt-scripted-modules/TotalSegmentator.py”, line 264, in onApplyButton

self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),

File “C:/Users/sain/Desktop/3DSilcer/Slicer 5.3.0/slicer.org/Extensions-31734/TotalSegmentator/lib/Slicer-5.3/qt-scripted-modules/TotalSegmentator.py”, line 799, in process

self.logProcessOutput(proc)

File “C:/Users/sain/Desktop/3DSilcer/Slicer 5.3.0/slicer.org/Extensions-31734/TotalSegmentator/lib/Slicer-5.3/qt-scripted-modules/TotalSegmentator.py”, line 692, in logProcessOutput

raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)

subprocess.CalledProcessError: Command ‘[‘C:/Users/sain/Desktop/3DSilcer/Slicer 5.3.0/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\sain\Desktop\3DSilcer\Slicer 5.3.0\lib\Python\Scripts\TotalSegmentator’, ‘-i’, ‘C:/Users/sain/AppData/Local/Temp/Slicer/__SlicerTemp__2023-05-10_10+01+57.716/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/sain/AppData/Local/Temp/Slicer/__SlicerTemp__2023-05-10_10+01+57.716/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 1.

44

This indicates that TotalSegmentator could not download the segmentation model weights from the internet. You are either not connected to the internet or firewall/proxy server prevents you from accessing the server.

You can either fix your internet connection (you may need to use VPN if you are in China, etc.) or download the model weights manually (see for example Run TotalSegmentator error · Issue #93 · wasserth/TotalSegmentator · GitHub and Use pre-downloaded weights in containerised implementation · Issue #60 · wasserth/TotalSegmentator · GitHub).

45

I download the model weights and paste files to the 3d_fullres folder.
It’s working now. Thank you!

2 Likes