Total Segmentor Lung Basic BUG report on Version 5.2.2 while working perfectly on 5.2.1

Khaldoun · March 8, 2023, 8:04pm

Operating system:: Windows 10 Professionnel
Intel(R) Core™ i5-10505 CPU @ 3.20GHz 3.19 GHz
16Go RAM
Slicer version:5.2.2
Expected behavior:Should be working as well as on version 5.2.1 installed on the same computer using the fast method as there is no CUDA and no GPU intalled
Actual behavior:: Bug report with 5.2.2 giving this followinf message:
Failed to compute results: Command ‘[‘C:/Users/g-tnn5319433pc/AppData/Local/NA-MIC/Slicer 5.2.2/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\g-tnn5319433pc\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Python\Scripts\TotalSegmentator’, ‘-i’, ‘C:/Users/g-tnn5319433pc/AppData/Local/Temp/Slicer/__SlicerTemp__2023-03-08_20+56+50.090/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/g-tnn5319433pc/AppData/Local/Temp/Slicer/__SlicerTemp__2023-03-08_20+56+50.090/segmentation’, ‘–ml’, ‘–task’, ‘total’]’ returned non-zero exit status 2.

thank you very much for your kind help
Khaldoun

rbumm · March 8, 2023, 8:57pm

You must install SlicerPytotch first and install Pytorch.
Then Restart.
The Use TotalSegmentator extension with itself installs TotalsSegmentator and sometimes finish with such an error message.
Restart Slicer, and run TS a second time, that usually fixes it.

jamesobutler · March 8, 2023, 11:42pm

@rbumm When you install the Slicer TotalSegmentor extension, doesn’t it automatically install the Slicer PyTorch extension dependency?

What situations require the user to manually do the process to install PyTorch?

rbumm · March 9, 2023, 6:59am

You are right, this step is done automatically.

If I just install a TS extension in a fresh 3D Slicer 5.2.2, load a dataset and press “Apply” I still get

upon the first try.

Any second run or a run after a 3D Slicer restart will succeed.

jamesobutler · March 13, 2023, 9:33pm

I am observing an error with the TotalSegmentor (like what is shown in the above image) install due to SlicerTotalSegmentor pointing to an older TotalSegmentor version.

A TotalSegmentor dependency incorrectly specified to install sklearn from PyPI instead of scikit-learn, and TotalSegmentor updated the dependency with a fix.

github.com/jamesobutler/SlicerTotalSegmentator

ENH: Install specific TotalSegmentator Python package version

committed 08:33PM - 16 Jan 23 UTC

rbumm

+44 -11

Until now, there was an option to install latest TotalSegmentator Python package… from GitHub. However, since the download URL was always the same, pip always used the same existing package in the cache (did not retrieve the latest content of the URL). There were also issues with options and behavior changing significantly between TotalSegmentator Python package versions, so updating the package separately from the Slicer module appeared to be risky. Therefore, behavior of the module is now changed so that the required TotalSegmentator Python package version (defined by download URL) is specified in the module logic constructor. When segmentation is started then the package version is checked and the package is updated if needed. An option for forced reinstallation was kept for troubleshooting and restoration of corrupted installations.

@rbumm @lassoan Is there a specific need to continue using TotalSegmentor as of ecf84f9? Would it be possible to upgrade this to the v1.5.3 tag which appears to contain the sklearn fix?

lassoan · March 13, 2023, 9:57pm

The current version already contains the sklearn fix (that allowed thousands of users successfully using TotalSegmentator). That said, if you tested this new hash and everything seems to work then there is no problem with updating the git hash. Please submit a pull request! Thank you.

I don’t trust the git tag, as it can be moved to a different version and pip will not notice it. So, please use a git hash (you can add the git label as a comment).

jamesobutler · March 13, 2023, 10:51pm

github.com

lassoan/SlicerTotalSegmentator/blob/fe5c538c8afee20f822c7a3e3075ff90fe9b1893/TotalSegmentator/TotalSegmentator.py#L301


      
          """
          
          def __init__(self):
              """
              Called when the logic class is instantiated. Can be used for initializing member variables.
              """
              from collections import OrderedDict
          
              ScriptedLoadableModuleLogic.__init__(self)
          
              self.totalSegmentatorPythonPackageDownloadUrl = "https://github.com/wasserth/TotalSegmentator/archive/ecf84f9e59b84dddb447e2b13542f58c29ee4c6a.zip"
          
              self.logCallback = None
              self.clearOutputFolder = True
              self.useStandardSegmentNames = True
          
              self.tasks = OrderedDict()
              self.tasks['total'] = {'label': 'total', 'supportsFast': True, 'supportsMultiLabel': True}
              self.tasks['lung_vessels'] = {'label': 'lung vessels', 'requiresPreSegmentation': True}
              self.tasks['cerebral_bleed'] = {'label': 'cerebral bleed', 'requiresPreSegmentation': True, 'supportsMultiLabel': True}
              self.tasks['hip_implant'] = {'label': 'hip implant', 'requiresPreSegmentation': True, 'supportsMultiLabel': True}

^This hash of TotalSegmentor produced an exit error code 1 associated with trying to install the sklearn from PyPI instead of scikit-learn. I did not previously have TotalSegmentor installed in Slicer 5.2.2.

jamesobutler · March 13, 2023, 11:55pm

With the currently used TotalSegmentor at ecf84f9 it specifies a hard version requirement of a dependency that then specifies sklearn instead of scikit-learn. This dependency at nnunet-customized==1.2 includes the fix, but pip —upgrade is not going to make that upgrade since a specific version of this dependency is stated as being required. Maybe this exit code for sklearn doesn’t stop TotalSegmentor from working, but does show as an exit code on first running TotalSegmentor when it gets installed.

github.com

wasserth/TotalSegmentator/blob/ecf84f9e59b84dddb447e2b13542f58c29ee4c6a/setup.py#L27


      
              # https://github.com/SimpleITK/SimpleITK/issues/1433
              'SimpleITK',
              'nibabel>=2.3.0',
              'tqdm>=4.45.0',
              'p_tqdm',
              'xvfbwrapper',
              'fury',
              'batchgenerators==0.21',
              # This does not work if want to upload to pypi
              # 'nnunet @ git+https://github.com/wasserth/nnUNet_cust@working_2022_03_18#egg=nnUNet'
              'nnunet-customized==1.1',
              'requests'
          ],
          zip_safe=False,
          classifiers=[
              'Intended Audience :: Science/Research',
              'Programming Language :: Python',
              'Topic :: Scientific/Engineering',
              'Operating System :: Unix',
              'Operating System :: MacOS'
          ],

Xref Update nnunet-customized to use scikit-learn instead of sklearn · Issue #72 · wasserth/TotalSegmentator · GitHub

lassoan · March 14, 2023, 2:57pm

Thanks for the investigation. Yes, probably scikit-learn is actually not needed (similarly as matplotlib and other dependencies are not used either).

@rbumm Created a PR to update to TotalSegmentator Python package and it has been merged.

jamesobutler · March 14, 2023, 4:52pm

I’ve written up the following issue report about errors installing TotalSegmentor python dependencies that results in TotalSegmentor not running the first time. Upon restarting Slicer, it will detect that the TotalSegmentor python package is present and will proceed normally.

github.com/lassoan/SlicerTotalSegmentator

SlicerTotalSegmentor fails on initial apply

opened 04:15PM - 14 Mar 23 UTC

closed 03:37AM - 05 Apr 23 UTC

jamesobutler

I'm currently using Slicer 5.2.2, have SlicerPyTorch installed and pointing to S…licerTotalSegmentor as of https://github.com/lassoan/SlicerTotalSegmentator/commit/493fa5bcbb75267e21ec086f95d0eb01ec1562a5. I start Slicer fresh, and when I go into TotalSegmentor and press apply, it appropriate warns that PyTorch needs to be downloaded and installed and then it installs the TotalSegmentor package. However I observe that the install process uninstall `scipy` 1.9.2 that is included as part of Slicer 5.2.2 and it installs `scipy` 1.9.1. This produces an exit code that results in TotalSegmentor not running. Is it expected for the uninstall/install of `scipy` to be successful in Slicer? If I close Slicer, reopen and then press "Apply" in TotalSegmentor then it is successful. Is access denied because the `scipy` package is in-use as it has been [imported in Slicer on startup](https://github.com/Slicer/Slicer/blob/fb46bd16846dc7c7a69c398aef0fc3baf533905e/Base/Python/slicer/__init__.py#L68-L69)? ``` ERROR: Could not install packages due to an OSError: [WinError 5] Access is denied: 'C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\lib\\Python\\Lib\\site-packages\\~cipy\\_lib\\_ccallback_c.cp39-win_amd64.pyd' Consider using the `--user` option or check the permissions. ``` ![image](https://user-images.githubusercontent.com/15837524/225063222-ddf680f7-0caf-4d1e-bf2d-2e652e463fc6.png) Additional FYI: The latest `torch 2.0.0` was downloaded and installed here. <details> <summary>See full pip output here</summary> Python 3.9.10 (main, Feb 22 2023, 01:07:37) [MSC v.1930 64 bit (AMD64)] on win32 >>> Collecting light-the-torch>=0.5 Downloading light_the_torch-0.7.1-py3-none-any.whl (14 kB) Requirement already satisfied: pip<23.1,>=22.3 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from light-the-torch>=0.5) (23.0) Installing collected packages: light-the-torch WARNING: The script ltt.exe is installed in 'C:\Users\butlej30383\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Python\Scripts' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed light-the-torch-0.7.1 [notice] A new release of pip is available: 23.0 -> 23.0.1 [notice] To update, run: python-real.exe -m pip install --upgrade pip Collecting torch Downloading https://download.pytorch.org/whl/cu118/torch-2.0.0%2Bcu118-cp39-cp39-win_amd64.whl (2611.4 MB) ---------------------------------------- 2.6/2.6 GB 1.7 MB/s eta 0:00:00 Collecting jinja2 Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB) -------------------------------------- 133.1/133.1 kB 1.6 MB/s eta 0:00:00 Collecting typing-extensions Downloading typing_extensions-4.5.0-py3-none-any.whl (27 kB) Collecting filelock Downloading filelock-3.9.1-py3-none-any.whl (9.7 kB) Collecting networkx Downloading networkx-3.0-py3-none-any.whl (2.0 MB) ---------------------------------------- 2.0/2.0 MB 10.0 MB/s eta 0:00:00 Collecting sympy Downloading sympy-1.11.1-py3-none-any.whl (6.5 MB) ---------------------------------------- 6.5/6.5 MB 29.5 MB/s eta 0:00:00 Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.2-cp39-cp39-win_amd64.whl (16 kB) Collecting mpmath>=0.19 Downloading mpmath-1.3.0-py3-none-any.whl (536 kB) ------------------------------------- 536.2/536.2 kB 32.9 MB/s eta 0:00:00 Installing collected packages: mpmath, typing-extensions, sympy, networkx, MarkupSafe, filelock, jinja2, torch WARNING: The script isympy.exe is installed in 'C:\Users\butlej30383\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Python\Scripts' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. WARNING: The scripts convert-caffe2-to-onnx.exe, convert-onnx-to-caffe2.exe and torchrun.exe are installed in 'C:\Users\butlej30383\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Python\Scripts' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed MarkupSafe-2.1.2 filelock-3.9.1 jinja2-3.1.2 mpmath-1.3.0 networkx-3.0 sympy-1.11.1 torch-2.0.0+cu118 typing-extensions-4.5.0 [notice] A new release of pip is available: 23.0 -> 23.0.1 [notice] To update, run: python-real.exe -m pip install --upgrade pip Collecting matplotlib Downloading matplotlib-3.7.1-cp39-cp39-win_amd64.whl (7.6 MB) ---------------------------------------- 7.6/7.6 MB 18.8 MB/s eta 0:00:00 Collecting python-dateutil>=2.7 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) -------------------------------------- 247.7/247.7 kB 7.7 MB/s eta 0:00:00 Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.4.4-cp39-cp39-win_amd64.whl (55 kB) ---------------------------------------- 55.4/55.4 kB 1.5 MB/s eta 0:00:00 Collecting fonttools>=4.22.0 Downloading fonttools-4.39.0-py3-none-any.whl (1.0 MB) ---------------------------------------- 1.0/1.0 MB 12.7 MB/s eta 0:00:00 Collecting cycler>=0.10 Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB) Requirement already satisfied: pillow>=6.2.0 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from matplotlib) (9.4.0) Requirement already satisfied: pyparsing>=2.3.1 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from matplotlib) (3.0.9) Requirement already satisfied: packaging>=20.0 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from matplotlib) (23.0) Collecting importlib-resources>=3.2.0 Downloading importlib_resources-5.12.0-py3-none-any.whl (36 kB) Requirement already satisfied: numpy>=1.20 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from matplotlib) (1.23.4) Collecting contourpy>=1.0.1 Downloading contourpy-1.0.7-cp39-cp39-win_amd64.whl (160 kB) -------------------------------------- 160.2/160.2 kB 3.2 MB/s eta 0:00:00 Collecting zipp>=3.1.0 Downloading zipp-3.15.0-py3-none-any.whl (6.8 kB) Requirement already satisfied: six>=1.5 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from python-dateutil>=2.7->matplotlib) (1.16.0) Installing collected packages: zipp, python-dateutil, kiwisolver, fonttools, cycler, contourpy, importlib-resources, matplotlib WARNING: The scripts fonttools.exe, pyftmerge.exe, pyftsubset.exe and ttx.exe are installed in 'C:\Users\butlej30383\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Python\Scripts' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed contourpy-1.0.7 cycler-0.11.0 fonttools-4.39.0 importlib-resources-5.12.0 kiwisolver-1.4.4 matplotlib-3.7.1 python-dateutil-2.8.2 zipp-3.15.0 [notice] A new release of pip is available: 23.0 -> 23.0.1 [notice] To update, run: python-real.exe -m pip install --upgrade pip Collecting https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip Downloading https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip - 5.5 MB 16.0 MB/s 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: numpy in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from TotalSegmentator==1.5.3) (1.23.4) Collecting psutil Downloading psutil-5.9.4-cp36-abi3-win_amd64.whl (252 kB) -------------------------------------- 252.5/252.5 kB 2.6 MB/s eta 0:00:00 Requirement already satisfied: SimpleITK in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from TotalSegmentator==1.5.3) (2.2.0rc2.dev368) Collecting nibabel>=2.3.0 Downloading nibabel-5.0.1-py3-none-any.whl (3.3 MB) ---------------------------------------- 3.3/3.3 MB 17.4 MB/s eta 0:00:00 Collecting tqdm>=4.45.0 Downloading tqdm-4.65.0-py3-none-any.whl (77 kB) ---------------------------------------- 77.1/77.1 kB ? eta 0:00:00 Collecting p_tqdm Downloading p_tqdm-1.4.0.tar.gz (5.2 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting xvfbwrapper Downloading xvfbwrapper-0.2.9.tar.gz (5.6 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting fury Downloading fury-0.8.0-py3-none-any.whl (349 kB) ------------------------------------- 349.2/349.2 kB 22.6 MB/s eta 0:00:00 Collecting batchgenerators==0.21 Downloading batchgenerators-0.21-py3-none-any.whl (74 kB) ---------------------------------------- 74.7/74.7 kB ? eta 0:00:00 Collecting nnunet-customized==1.2 Downloading nnunet_customized-1.2-py3-none-any.whl (474 kB) ------------------------------------- 474.0/474.0 kB 29.0 MB/s eta 0:00:00 Requirement already satisfied: requests in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from TotalSegmentator==1.5.3) (2.28.2) Requirement already satisfied: scipy in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from batchgenerators==0.21->TotalSegmentator==1.5.3) (1.9.2) Collecting future Downloading future-0.18.3.tar.gz (840 kB) ------------------------------------- 840.9/840.9 kB 51.9 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting scikit-learn Downloading scikit_learn-1.2.2-cp39-cp39-win_amd64.whl (8.4 MB) ---------------------------------------- 8.4/8.4 MB 38.2 MB/s eta 0:00:00 Collecting scikit-image Downloading scikit_image-0.20.0-cp39-cp39-win_amd64.whl (23.9 MB) --------------------------------------- 23.9/23.9 MB 28.4 MB/s eta 0:00:00 Collecting threadpoolctl Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Requirement already satisfied: pillow>=7.1.2 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from batchgenerators==0.21->TotalSegmentator==1.5.3) (9.4.0) Collecting unittest2 Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB) ---------------------------------------- 96.4/96.4 kB ? eta 0:00:00 Collecting dicom2nifti Downloading dicom2nifti-2.4.8-py3-none-any.whl (43 kB) ---------------------------------------- 43.6/43.6 kB ? eta 0:00:00 Collecting pandas Downloading pandas-1.5.3-cp39-cp39-win_amd64.whl (10.9 MB) --------------------------------------- 10.9/10.9 MB 54.4 MB/s eta 0:00:00 Collecting tifffile Downloading tifffile-2023.2.28-py3-none-any.whl (216 kB) ------------------------------------- 216.4/216.4 kB 12.9 MB/s eta 0:00:00 Collecting medpy Downloading MedPy-0.4.0.tar.gz (151 kB) ---------------------------------------- 151.8/151.8 kB ? eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: torch>=1.6.0a in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from nnunet-customized==1.2->TotalSegmentator==1.5.3) (2.0.0+cu118) Requirement already satisfied: packaging>=17 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from nibabel>=2.3.0->TotalSegmentator==1.5.3) (23.0) Requirement already satisfied: setuptools in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from nibabel>=2.3.0->TotalSegmentator==1.5.3) (67.0.0) Collecting colorama Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB) Requirement already satisfied: vtk>=9.1.0 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from fury->TotalSegmentator==1.5.3) (9.1.20220125) Collecting pathos>=0.2.5 Downloading pathos-0.3.0-py3-none-any.whl (79 kB) ---------------------------------------- 79.8/79.8 kB ? eta 0:00:00 Requirement already satisfied: six>=1.13.0 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from p_tqdm->TotalSegmentator==1.5.3) (1.16.0) Requirement already satisfied: idna<4,>=2.5 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from requests->TotalSegmentator==1.5.3) (3.4) Requirement already satisfied: certifi>=2017.4.17 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from requests->TotalSegmentator==1.5.3) (2022.12.7) Requirement already satisfied: charset-normalizer<4,>=2 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from requests->TotalSegmentator==1.5.3) (3.0.1) Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from requests->TotalSegmentator==1.5.3) (1.26.14) Collecting multiprocess>=0.70.14 Downloading multiprocess-0.70.14-py39-none-any.whl (132 kB) ---------------------------------------- 132.9/132.9 kB ? eta 0:00:00 Collecting ppft>=1.7.6.6 Downloading ppft-1.7.6.6-py3-none-any.whl (52 kB) ---------------------------------------- 52.8/52.8 kB ? eta 0:00:00 Collecting dill>=0.3.6 Downloading dill-0.3.6-py3-none-any.whl (110 kB) ---------------------------------------- 110.5/110.5 kB ? eta 0:00:00 Collecting pox>=0.3.2 Downloading pox-0.3.2-py3-none-any.whl (29 kB) Collecting lazy_loader>=0.1 Downloading lazy_loader-0.1-py3-none-any.whl (8.6 kB) Collecting PyWavelets>=1.1.1 Downloading PyWavelets-1.4.1-cp39-cp39-win_amd64.whl (4.2 MB) ---------------------------------------- 4.2/4.2 MB 38.2 MB/s eta 0:00:00 Requirement already satisfied: networkx>=2.8 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from scikit-image->batchgenerators==0.21->TotalSegmentator==1.5.3) (3.0) Collecting scipy Downloading scipy-1.9.1-cp39-cp39-win_amd64.whl (38.6 MB) --------------------------------------- 38.6/38.6 MB 40.9 MB/s eta 0:00:00 Collecting imageio>=2.4.1 Downloading imageio-2.26.0-py3-none-any.whl (3.4 MB) ---------------------------------------- 3.4/3.4 MB 30.8 MB/s eta 0:00:00 Requirement already satisfied: typing-extensions in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from torch>=1.6.0a->nnunet-customized==1.2->TotalSegmentator==1.5.3) (4.5.0) Requirement already satisfied: sympy in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from torch>=1.6.0a->nnunet-customized==1.2->TotalSegmentator==1.5.3) (1.11.1) Requirement already satisfied: jinja2 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from torch>=1.6.0a->nnunet-customized==1.2->TotalSegmentator==1.5.3) (3.1.2) Requirement already satisfied: filelock in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from torch>=1.6.0a->nnunet-customized==1.2->TotalSegmentator==1.5.3) (3.9.1) Collecting python-gdcm Downloading python_gdcm-3.0.21-cp39-cp39-win_amd64.whl (27.2 MB) --------------------------------------- 27.2/27.2 MB 36.4 MB/s eta 0:00:00 Requirement already satisfied: pydicom>=2.2.0 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from dicom2nifti->nnunet-customized==1.2->TotalSegmentator==1.5.3) (2.3.1) Requirement already satisfied: python-dateutil>=2.8.1 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from pandas->nnunet-customized==1.2->TotalSegmentator==1.5.3) (2.8.2) Collecting pytz>=2020.1 Downloading pytz-2022.7.1-py2.py3-none-any.whl (499 kB) ------------------------------------- 499.4/499.4 kB 15.8 MB/s eta 0:00:00 Collecting joblib>=1.1.1 Downloading joblib-1.2.0-py3-none-any.whl (297 kB) ------------------------------------- 298.0/298.0 kB 18.0 MB/s eta 0:00:00 Collecting argparse Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB) Collecting traceback2 Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB) Requirement already satisfied: MarkupSafe>=2.0 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from jinja2->torch>=1.6.0a->nnunet-customized==1.2->TotalSegmentator==1.5.3) (2.1.2) Requirement already satisfied: mpmath>=0.19 in c:\users\butlej30383\appdata\local\na-mic\slicer 5.2.2\lib\python\lib\site-packages (from sympy->torch>=1.6.0a->nnunet-customized==1.2->TotalSegmentator==1.5.3) (1.3.0) Collecting linecache2 Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB) Building wheels for collected packages: TotalSegmentator, p_tqdm, xvfbwrapper, future, medpy Building wheel for TotalSegmentator (setup.py): started Building wheel for TotalSegmentator (setup.py): finished with status 'done' Created wheel for TotalSegmentator: filename=TotalSegmentator-1.5.3-py3-none-any.whl size=40473 sha256=72631d27e92da70d44e97e4309a78d20e685ff9af743f96d7e69538a655f33f7 Stored in directory: C:\Users\butlej30383\AppData\Local\Temp\pip-ephem-wheel-cache-98sqy9xm\wheels\9f\4f\c3\aa92a6088ded23ae736534c7fd546ac5aec3409f87bbed6852 Building wheel for p_tqdm (setup.py): started Building wheel for p_tqdm (setup.py): finished with status 'done' Created wheel for p_tqdm: filename=p_tqdm-1.4.0-py3-none-any.whl size=5411 sha256=fa28bb84f74c368e3ca9f728cac1ce3da2df3fb07f95dcf27cf8d23c317ab512 Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\53\8b\76\19cce68cdb3253aee026a593ec9bc772607b85193cf65e1f53 Building wheel for xvfbwrapper (setup.py): started Building wheel for xvfbwrapper (setup.py): finished with status 'done' Created wheel for xvfbwrapper: filename=xvfbwrapper-0.2.9-py3-none-any.whl size=5027 sha256=b15a6b7c25585d54d8fb6e75a0c52c862db0ca6335cbbb1f53a9fb4607d54d0d Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\aa\09\0e\c0fa4c721cfb0a003121597a24181add912b7488054d2311ad Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492055 sha256=e5d845853ca1d4176cfadcbc5699dbe1277875648cb957ad91f9787813b5c77a Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\bf\5d\6a\2e53874f7ec4e2bede522385439531fafec8fafe005b5c3d1b Building wheel for medpy (setup.py): started Building wheel for medpy (setup.py): finished with status 'done' Created wheel for medpy: filename=MedPy-0.4.0-py3-none-any.whl size=215911 sha256=47f6a0c552cdc868104caf188bd34e85fbd5fd46a2882b6893bc782b1b948d8c Stored in directory: c:\users\butlej30383\appdata\local\pip\cache\wheels\41\46\a2\7c585b78f216a3dd8723dbab5f439822fa5dfbff563757a49e Successfully built TotalSegmentator p_tqdm xvfbwrapper future medpy Installing collected packages: xvfbwrapper, pytz, linecache2, argparse, traceback2, tifffile, threadpoolctl, scipy, PyWavelets, python-gdcm, psutil, ppft, pox, nibabel, lazy_loader, joblib, imageio, future, dill, colorama, unittest2, tqdm, scikit-learn, scikit-image, pandas, multiprocess, medpy, fury, dicom2nifti, pathos, batchgenerators, p_tqdm, nnunet-customized, TotalSegmentator WARNING: The scripts lsm2bin.exe, tiff2fsspec.exe, tiffcomment.exe and tifffile.exe are installed in 'C:\Users\butlej30383\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Python\Scripts' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Attempting uninstall: scipy Found existing installation: scipy 1.9.2 Uninstalling scipy-1.9.2: Successfully uninstalled scipy-1.9.2 ERROR: Could not install packages due to an OSError: [WinError 5] Access is denied: 'C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\lib\\Python\\Lib\\site-packages\\~cipy\\_lib\\_ccallback_c.cp39-win_amd64.pyd' Consider using the `--user` option or check the permissions. [notice] A new release of pip is available: 23.0 -> 23.0.1 [notice] To update, run: python-real.exe -m pip install --upgrade pip [Python] Failed to compute results. [Python] Command '['C:/Users/butlej30383/AppData/Local/NA-MIC/Slicer 5.2.2/bin/../bin\\PythonSlicer.EXE', '-m', 'pip', 'install', 'https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip']' returned non-zero exit status 1. Traceback (most recent call last): File "C:/GitHub/SlicerTotalSegmentator/TotalSegmentator/TotalSegmentator.py", line 255, in onApplyButton self.logic.setupPythonRequirements() File "C:/GitHub/SlicerTotalSegmentator/TotalSegmentator/TotalSegmentator.py", line 624, in setupPythonRequirements slicer.util.pip_install(self.totalSegmentatorPythonPackageDownloadUrl) File "C:\Users\butlej30383\AppData\Local\NA-MIC\Slicer 5.2.2\bin\Python\slicer\util.py", line 3578, in pip_install _executePythonModule('pip', args) File "C:\Users\butlej30383\AppData\Local\NA-MIC\Slicer 5.2.2\bin\Python\slicer\util.py", line 3540, in _executePythonModule logProcessOutput(proc) File "C:\Users\butlej30383\AppData\Local\NA-MIC\Slicer 5.2.2\bin\Python\slicer\util.py", line 3509, in logProcessOutput raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr) subprocess.CalledProcessError: Command '['C:/Users/butlej30383/AppData/Local/NA-MIC/Slicer 5.2.2/bin/../bin\\PythonSlicer.EXE', '-m', 'pip', 'install', 'https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip']' returned non-zero exit status 1. </details>

rbumm · March 14, 2023, 7:45pm

@lassoan can we not just force a restart after TS installation?

Topic		Replies	Views
Total segmentator issue Support	5	526	April 3, 2023
Pytorch extension installation Support	6	464	August 4, 2023
Unable to use Total Segmentator in Slicer 5.2.2 Support segmentation	1	368	March 29, 2023
TotalSegmentator Support segmentation	4	315	November 17, 2023
Total Segmenter cannot detect my GPU (1080ti x 2) Support	4	951	June 5, 2023

Total Segmentor Lung Basic BUG report on Version 5.2.2 while working perfectly on 5.2.1

Related Topics