# TotalSegmentator installation problem due to Zenodo connection error

**URL:** <https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [February 8, 2023, 1:55pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705 "2023-02-08T13:55:10Z")\
**Posts on this page:** 11\
**Page:** 1

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**Author:** ![zhangliang](https://avatars.discourse-cdn.com/v4/letter/z/ee59a6/32.png) [@zhangliang](https://discourse.slicer.org/u/zhangliang)\
**Post date:** [February 8, 2023, 1:55pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/1 "2023-02-08T13:55:10Z")

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I have some problems installing TotalSegmentator. Let me try to describe it clearly. I hope to get your help.  
My device：DELL windows 10 NVIDIA GeForceRTX3060 ,Display Memory: 28386 MB

pyTorch :version 1.13+cu117  
NVidia driver: version 512.77

=========  
Processing started

Writing input file to C:/Users/Administrator/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-02-08\_16+16+43.146/total-segmentator-input.nii

Creating segmentations with TotalSegmentator AI…

Total Segmentator arguments: [‘-i’, ‘C:/Users/Administrator/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-02-08\_16+16+43.146/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/Administrator/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-02-08\_16+16+43.146/segmentation’, ‘–ml’, ‘–task’, ‘total’]

If you use this tool please cite: [[2208.05868] TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://doi.org/10.48550/arXiv.2208.05868)

Downloading pretrained weights for Task 251 (~230MB) …

Traceback (most recent call last):

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connection.py”, line 174, in \_new\_conn

conn = connection.create\_connection(

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\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:\ProgramData\NA-MIC\Slicer 5.2.1\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:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 703, in urlopen

httplib\_response = self.\_make\_request(

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 386, in \_make\_request

self.\_validate\_conn(conn)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 1042, in \_validate\_conn

conn.connect()

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connection.py”, line 358, in connect

self.sock = conn = self.\_new\_conn()

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connection.py”, line 186, in \_new\_conn

raise NewConnectionError(

urllib3.exceptions.NewConnectionError: \<urllib3.connection.HTTPSConnection object at 0x0000023943A0D700\>: 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:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\adapters.py”, line 489, in send

resp = conn.urlopen(

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 787, in urlopen

retries = retries.increment(

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\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](http://zenodo.org/)’, port=443): Max retries exceeded with url: /record/6802342/files/Task251\_TotalSegmentator\_part1\_organs\_1139subj.zip?download=1 (Caused by NewConnectionError(‘\<urllib3.connection.HTTPSConnection object at 0x0000023943A0D700\>: 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:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Scripts\TotalSegmentator”, line 241, in

main()

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Scripts\TotalSegmentator”, line 200, in main

download\_pretrained\_weights(tid)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\totalsegmentator\libs.py”, line 175, in download\_pretrained\_weights

download\_url\_and\_unpack(WEIGHTS\_URL, config\_dir)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\totalsegmentator\libs.py”, line 69, in download\_url\_and\_unpack

raise e

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\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:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\api.py”, line 73, in get

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

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\api.py”, line 59, in request

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

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\sessions.py”, line 587, in request

resp = self.send(prep, \*\*send\_kwargs)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\sessions.py”, line 701, in send

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

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\adapters.py”, line 565, in send

raise ConnectionError(e, request=request)

requests.exceptions.ConnectionError: HTTPSConnectionPool(host=‘[zenodo.org](http://zenodo.org/)’, port=443): Max retries exceeded with url: /record/6802342/files/Task251\_TotalSegmentator\_part1\_organs\_1139subj.zip?download=1 (Caused by NewConnectionError(‘\<urllib3.connection.HTTPSConnection object at 0x0000023943A0D700\>: Failed to establish a new connection: [Errno 11004] getaddrinfo failed’))

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [February 8, 2023, 1:57pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/2 "2023-02-08T13:57:35Z")

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It looks like the file download failed. I have gotten timeouts from [zenodo.org](http://zenodo.org) before using a web browser so I’m sure the same thing would happen from time to time using the programatic interface too. Probably try again in a few hours or days when it’s less busy.

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**Author:** ![zhangliang](https://avatars.discourse-cdn.com/v4/letter/z/ee59a6/32.png) [@zhangliang](https://discourse.slicer.org/u/zhangliang)\
**Post date:** [February 8, 2023, 2:07pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/3 "2023-02-08T14:07:37Z")

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Thank you. It’s really unstable. I have tested many times and always failed, using VPN or not ，using different WiFi at different times. 3d\_ The fullres folder is always empty.Is there any other way? For example, download some files manually.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [February 8, 2023, 2:33pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/4 "2023-02-08T14:33:21Z")

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I was able to install TotalSegmentator yesterday on a new windows machine. It took a while but it succeeded. I don’t know if it matters where the connection comes from; in my experience it is the server just being overwhelmed from time to time. If this keeps up we might want to find a way to mirror the files somewhere else (google drive, github release, etc).

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 8, 2023, 3:19pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/5 "2023-02-08T15:19:33Z")

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Yesterday our collaborators from Hungary reported Zenodo servers timing out, too.

@zhangliang could you please [report this problem in the TotalSegmentator Python package repository](https://github.com/wasserth/TotalSegmentator/issues)? It is important for the developers to know about this issue and start thinking about alternative hosting options.

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**Author:** ![zhangliang](https://avatars.discourse-cdn.com/v4/letter/z/ee59a6/32.png) [@zhangliang](https://discourse.slicer.org/u/zhangliang)\
**Post date:** [February 9, 2023, 11:10am UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/6 "2023-02-09T11:10:16Z")

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OK, I have submitted the problem as required, and I look forward to solving it.

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**Author:** ![zhang\_ming](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/zhang_ming/32/15790_2.png) [@zhang\_ming](https://discourse.slicer.org/u/zhang_ming)\
**Post date:** [February 20, 2023, 12:09pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/7 "2023-02-20T12:09:46Z")

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I have met up with this problem too. may local weights added to slicer plugin, and upload the weights to google drive ?

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**Author:** ![zhangliang](https://avatars.discourse-cdn.com/v4/letter/z/ee59a6/32.png) [@zhangliang](https://discourse.slicer.org/u/zhangliang)\
**Post date:** [February 22, 2023, 8:17am UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/8 "2023-02-22T08:17:56Z")

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Hello, I think I have solved this problem. You can manually download the zip file and put it in the specified location. You can sign in [http://zenodo.org/](http://zenodo.org/) And search for missing files

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**Author:** ![zhang\_ming](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/zhang_ming/32/15790_2.png) [@zhang\_ming](https://discourse.slicer.org/u/zhang_ming)\
**Post date:** [February 22, 2023, 11:22am UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/9 "2023-02-22T11:22:18Z")

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yes!!! I have download all this zip files manually, it worked

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 27, 2023, 12:35pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/10 "2023-02-27T12:35:24Z")

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2 posts were split to a new topic: [How to segment the tibia using TotalSegmentator?](https://discourse.slicer.org/t/how-to-segment-the-tibia-using-totalsegmentator/28065)

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<div class="post-metadata">

**Author:** ![xiaoli26](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/xiaoli26/32/65621_2.png) [@xiaoli26](https://discourse.slicer.org/u/xiaoli26)\
**Post date:** [April 14, 2023, 2:57pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705/11 "2023-04-14T14:57:41Z")

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C:\Users\XXX.totalsegmentator\nnunet\results\nnUNet\3d\_fullres

and it works, thx!