Errors for totalsegmentator

yf025 · March 27, 2023, 1:42am

I installed pytorch module and totalsegmentator in extensions manager then nii was imported ，but after I clicking “apply” and waiting for the process“TotalSegmentator Python package is required. Installing… (it may take several minutes)”，then the error info poped out。Need help to solve this，thx！
Here are the error infos。
Failed to compute results.
Command '[‘C:/ProgramData/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.

jamesobutler · March 27, 2023, 1:58am

Based on the provided information I believe this is the following issue linked below. The current workaround is to restart Slicer after the TotalSegmentor python package is installed and it should proceed successfully.

github.com/lassoan/SlicerTotalSegmentator

SlicerTotalSegmentor fails on initial apply

opened 04:15PM - 14 Mar 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>