*******************************
* Welcome to SCT installation *
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Checking OS type and version...

Darwin Dominics-MacBook-Pro-2.local 23.6.0 Darwin Kernel Version 23.6.0: Mon Jul 29 21:13:04 PDT 2024; root:xnu-10063.141.2~1/RELEASE_ARM64_T6020 arm64
ProductVersion:		14.6.1

Checking requirements...


OK!

Source files not present. Downloading source files (@ 6.5) to /var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/tmp.dRomOIgUAL/spinalcordtoolbox.
Cloning into '/var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/tmp.dRomOIgUAL/spinalcordtoolbox'...
Note: switching to '7a790312c7fea04880c9cce6667cbc3f56f00768'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false


SCT version ......... 6.5
Installation type ... package
Operating system .... osx (	14.6.1)
Shell config ........ /Users/dominicvhoule/.zshrc

SCT will be installed here: [/Users/dominicvhoule/sct_6.5]



Do you agree? [y]es/[n]o: 
Copying source files from /var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/tmp.dRomOIgUAL/spinalcordtoolbox to /Users/dominicvhoule/sct_6.5

................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Removing sct and isct softlink from /Users/dominicvhoule/sct_6.5/bin


rm -rf /Users/dominicvhoule/sct_6.5/python


mkdir -p /Users/dominicvhoule/sct_6.5/python


rm -rf /Users/dominicvhoule/sct_6.5/spinalcordtoolbox.egg-info


Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: 
Downloading Miniconda...


curl -sS -o /var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/tmp.dRomOIgUAL/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh


Installing Miniconda...


bash /var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/tmp.dRomOIgUAL/miniconda.sh -p /Users/dominicvhoule/sct_6.5/python -b -f

PREFIX=/Users/dominicvhoule/sct_6.5/python
Unpacking payload ...

Installing base environment...

Preparing transaction: ...working... done
Executing transaction: ...working... 
done
installation finished.

Creating conda environment...

Channels:
 - defaults
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/dominicvhoule/sct_6.5/python/envs/venv_sct

  added / updated specs:
    - python=3.9


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    pip-25.0                   |   py39hecd8cb5_0         2.3 MB
    python-3.9.21              |       hce00570_1        12.7 MB
    setuptools-75.8.0          |   py39hecd8cb5_0         1.6 MB
    wheel-0.45.1               |   py39hecd8cb5_0         117 KB
    ------------------------------------------------------------
                                           Total:        16.6 MB

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2024.12.31-hecd8cb5_0 
  libcxx             pkgs/main/osx-64::libcxx-14.0.6-h9765a3e_0 
  libffi             pkgs/main/osx-64::libffi-3.4.4-hecd8cb5_1 
  ncurses            pkgs/main/osx-64::ncurses-6.4-hcec6c5f_0 
  openssl            pkgs/main/osx-64::openssl-3.0.15-h46256e1_0 
  pip                pkgs/main/osx-64::pip-25.0-py39hecd8cb5_0 
  python             pkgs/main/osx-64::python-3.9.21-hce00570_1 
  readline           pkgs/main/osx-64::readline-8.2-hca72f7f_0 
  setuptools         pkgs/main/osx-64::setuptools-75.8.0-py39hecd8cb5_0 
  sqlite             pkgs/main/osx-64::sqlite-3.45.3-h6c40b1e_0 
  tk                 pkgs/main/osx-64::tk-8.6.14-h4d00af3_0 
  tzdata             pkgs/main/noarch::tzdata-2025a-h04d1e81_0 
  wheel              pkgs/main/osx-64::wheel-0.45.1-py39hecd8cb5_0 
  xz                 pkgs/main/osx-64::xz-5.4.6-h6c40b1e_1 
  zlib               pkgs/main/osx-64::zlib-1.2.13-h4b97444_1 



Downloading and Extracting Packages: ...working...
python-3.9.21        | 12.7 MB   |            |   0% 

pip-25.0             | 2.3 MB    |            |   0% 


setuptools-75.8.0    | 1.6 MB    |            |   0% 



wheel-0.45.1         | 117 KB    |            |   0% 



wheel-0.45.1         | 117 KB    | #3         |  14% 



wheel-0.45.1         | 117 KB    | ########## | 100% 


setuptools-75.8.0    | 1.6 MB    | 1          |   1% 
python-3.9.21        | 12.7 MB   |            |   0% 

pip-25.0             | 2.3 MB    |            |   1% 



wheel-0.45.1         | 117 KB    | ########## | 100% 


setuptools-75.8.0    | 1.6 MB    | #######2   |  72% 
python-3.9.21        | 12.7 MB   | 9          |   9% 

pip-25.0             | 2.3 MB    | ###7       |  37% 


setuptools-75.8.0    | 1.6 MB    | ########## | 100% 
python-3.9.21        | 12.7 MB   | ##7        |  28% 

pip-25.0             | 2.3 MB    | ########## | 100% 

pip-25.0             | 2.3 MB    | ########## | 100% 
python-3.9.21        | 12.7 MB   | ######2    |  63% 
python-3.9.21        | 12.7 MB   | #########4 |  95% 
python-3.9.21        | 12.7 MB   | ########## | 100% 


setuptools-75.8.0    | 1.6 MB    | ########## | 100% 

pip-25.0             | 2.3 MB    | ########## | 100% 
python-3.9.21        | 12.7 MB   | ########## | 100% 
                                                     

                                                     


                                                     



                                                      done
Preparing transaction: - \ done
Verifying transaction: / - \ | / - \ | / done
Executing transaction: \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
#
# To activate this environment, use
#
#     $ conda activate /Users/dominicvhoule/sct_6.5/python/envs/venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (25.0)
Collecting pip!=21.2.*
  Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 25.0
    Uninstalling pip-25.0:
      Successfully uninstalled pip-25.0
Successfully installed pip-25.0.1

Installing Python dependencies...


Using requirements-freeze.txt (release installation)

Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment
Collecting certifi
  Using cached certifi-2025.1.31-py3-none-any.whl.metadata (2.5 kB)
Collecting absl-py==2.1.0 (from -r requirements-freeze.txt (line 1))
  Using cached absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting acvl_utils==0.2 (from -r requirements-freeze.txt (line 2))
  Using cached acvl_utils-0.2-py3-none-any.whl
Collecting astor==0.8.1 (from -r requirements-freeze.txt (line 3))
  Using cached astor-0.8.1-py2.py3-none-any.whl.metadata (4.2 kB)
Collecting attrs==24.2.0 (from -r requirements-freeze.txt (line 4))
  Using cached attrs-24.2.0-py3-none-any.whl.metadata (11 kB)
Collecting batchgenerators==0.25.1 (from -r requirements-freeze.txt (line 5))
  Using cached batchgenerators-0.25.1-py3-none-any.whl
Collecting bids-validator==1.14.7.post0 (from -r requirements-freeze.txt (line 6))
  Using cached bids_validator-1.14.7.post0-py3-none-any.whl.metadata (39 kB)
Collecting bidsschematools==0.11.3.post3 (from -r requirements-freeze.txt (line 7))
  Using cached bidsschematools-0.11.3.post3-py3-none-any.whl.metadata (3.6 kB)
Collecting certifi
  Using cached certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
Collecting charset-normalizer==3.4.0 (from -r requirements-freeze.txt (line 9))
  Using cached charset_normalizer-3.4.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (34 kB)
Collecting click==8.1.7 (from -r requirements-freeze.txt (line 10))
  Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting coloredlogs==15.0.1 (from -r requirements-freeze.txt (line 11))
  Using cached coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB)
Collecting connected-components-3d==3.21.0 (from -r requirements-freeze.txt (line 12))
  Using cached connected_components_3d-3.21.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (32 kB)
Collecting contourpy==1.3.0 (from -r requirements-freeze.txt (line 13))
  Using cached contourpy-1.3.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (5.4 kB)
Collecting coverage==7.6.8 (from -r requirements-freeze.txt (line 14))
  Using cached coverage-7.6.8-cp39-cp39-macosx_10_9_x86_64.whl.metadata (8.2 kB)
Collecting csv-diff==1.2 (from -r requirements-freeze.txt (line 15))
  Using cached csv_diff-1.2-py3-none-any.whl.metadata (5.3 kB)
Collecting cycler==0.12.1 (from -r requirements-freeze.txt (line 16))
  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting Cython==3.0.11 (from -r requirements-freeze.txt (line 17))
  Using cached Cython-3.0.11-cp39-cp39-macosx_10_9_x86_64.whl.metadata (3.2 kB)
Collecting deepdiff==8.0.1 (from -r requirements-freeze.txt (line 18))
  Using cached deepdiff-8.0.1-py3-none-any.whl.metadata (8.5 kB)
Collecting Deprecated==1.2.15 (from -r requirements-freeze.txt (line 19))
  Using cached Deprecated-1.2.15-py2.py3-none-any.whl.metadata (5.5 kB)
Collecting dicom2nifti==2.5.0 (from -r requirements-freeze.txt (line 20))
  Using cached dicom2nifti-2.5.0-py3-none-any.whl.metadata (1.3 kB)
Collecting dictdiffer==0.9.0 (from -r requirements-freeze.txt (line 21))
  Using cached dictdiffer-0.9.0-py2.py3-none-any.whl.metadata (4.8 kB)
Collecting dipy==1.8.0 (from -r requirements-freeze.txt (line 22))
  Using cached dipy-1.8.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (8.6 kB)
Collecting docker-pycreds==0.4.0 (from -r requirements-freeze.txt (line 23))
  Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting docopt==0.6.2 (from -r requirements-freeze.txt (line 24))
  Using cached docopt-0.6.2-py2.py3-none-any.whl
Collecting dynamic_network_architectures==0.3.1 (from -r requirements-freeze.txt (line 25))
  Using cached dynamic_network_architectures-0.3.1-py3-none-any.whl
Collecting exceptiongroup==1.2.2 (from -r requirements-freeze.txt (line 26))
  Using cached exceptiongroup-1.2.2-py3-none-any.whl.metadata (6.6 kB)
Collecting filelock==3.16.1 (from -r requirements-freeze.txt (line 27))
  Using cached filelock-3.16.1-py3-none-any.whl.metadata (2.9 kB)
Collecting flatbuffers==24.3.25 (from -r requirements-freeze.txt (line 28))
  Using cached flatbuffers-24.3.25-py2.py3-none-any.whl.metadata (850 bytes)
Collecting fonttools==4.55.1 (from -r requirements-freeze.txt (line 29))
  Using cached fonttools-4.55.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (164 kB)
Collecting formulaic==0.3.4 (from -r requirements-freeze.txt (line 30))
  Using cached formulaic-0.3.4-py3-none-any.whl.metadata (5.6 kB)
Collecting fsspec==2024.10.0 (from -r requirements-freeze.txt (line 31))
  Using cached fsspec-2024.10.0-py3-none-any.whl.metadata (11 kB)
Collecting future==1.0.0 (from -r requirements-freeze.txt (line 32))
  Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
Collecting gitdb==4.0.11 (from -r requirements-freeze.txt (line 33))
  Using cached gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Collecting GitPython==3.1.43 (from -r requirements-freeze.txt (line 34))
  Using cached GitPython-3.1.43-py3-none-any.whl.metadata (13 kB)
Collecting graphviz==0.20.3 (from -r requirements-freeze.txt (line 35))
  Using cached graphviz-0.20.3-py3-none-any.whl.metadata (12 kB)
Collecting grpcio==1.68.1 (from -r requirements-freeze.txt (line 36))
  Using cached grpcio-1.68.1-cp39-cp39-macosx_10_9_universal2.whl.metadata (3.9 kB)
Collecting gryds==0.0.9 (from -r requirements-freeze.txt (line 37))
  Using cached gryds-0.0.9-py3-none-any.whl.metadata (1.0 kB)
Collecting h5py==3.12.1 (from -r requirements-freeze.txt (line 38))
  Using cached h5py-3.12.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.5 kB)
Collecting humanfriendly==10.0 (from -r requirements-freeze.txt (line 39))
  Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB)
Collecting humanize==4.11.0 (from -r requirements-freeze.txt (line 40))
  Using cached humanize-4.11.0-py3-none-any.whl.metadata (7.8 kB)
Collecting idna==3.10 (from -r requirements-freeze.txt (line 41))
  Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting imagecodecs==2024.9.22 (from -r requirements-freeze.txt (line 42))
  Using cached imagecodecs-2024.9.22-cp39-cp39-macosx_10_14_x86_64.whl.metadata (20 kB)
Collecting imageio==2.36.1 (from -r requirements-freeze.txt (line 43))
  Using cached imageio-2.36.1-py3-none-any.whl.metadata (5.2 kB)
Collecting importlib_metadata==8.5.0 (from -r requirements-freeze.txt (line 44))
  Using cached importlib_metadata-8.5.0-py3-none-any.whl.metadata (4.8 kB)
Collecting importlib_resources==6.4.5 (from -r requirements-freeze.txt (line 45))
  Using cached importlib_resources-6.4.5-py3-none-any.whl.metadata (4.0 kB)
Collecting iniconfig==2.0.0 (from -r requirements-freeze.txt (line 46))
  Using cached iniconfig-2.0.0-py3-none-any.whl.metadata (2.6 kB)
Collecting interface-meta==1.3.0 (from -r requirements-freeze.txt (line 47))
  Using cached interface_meta-1.3.0-py3-none-any.whl.metadata (6.7 kB)
Collecting ivadomed==2.9.10 (from -r requirements-freeze.txt (line 48))
  Using cached ivadomed-2.9.10-py3-none-any.whl.metadata (6.4 kB)
Collecting Jinja2==3.1.4 (from -r requirements-freeze.txt (line 49))
  Using cached https://download.pytorch.org/whl/Jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
Collecting joblib==1.4.2 (from -r requirements-freeze.txt (line 50))
  Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Collecting jsonschema==4.23.0 (from -r requirements-freeze.txt (line 51))
  Using cached jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB)
Collecting jsonschema-specifications==2024.10.1 (from -r requirements-freeze.txt (line 52))
  Using cached jsonschema_specifications-2024.10.1-py3-none-any.whl.metadata (3.0 kB)
Collecting kiwisolver==1.4.7 (from -r requirements-freeze.txt (line 53))
  Using cached kiwisolver-1.4.7-cp39-cp39-macosx_10_9_x86_64.whl.metadata (6.3 kB)
Collecting lazy_loader==0.4 (from -r requirements-freeze.txt (line 54))
  Using cached lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB)
Collecting linecache2==1.0.0 (from -r requirements-freeze.txt (line 55))
  Using cached linecache2-1.0.0-py2.py3-none-any.whl.metadata (1000 bytes)
Collecting loguru==0.7.2 (from -r requirements-freeze.txt (line 56))
  Using cached loguru-0.7.2-py3-none-any.whl.metadata (23 kB)
Collecting lxml==5.3.0 (from -r requirements-freeze.txt (line 57))
  Using cached lxml-5.3.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (3.8 kB)
Collecting Markdown==3.7 (from -r requirements-freeze.txt (line 58))
  Using cached Markdown-3.7-py3-none-any.whl.metadata (7.0 kB)
Collecting markdown-it-py==3.0.0 (from -r requirements-freeze.txt (line 59))
  Using cached markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting MarkupSafe==3.0.2 (from -r requirements-freeze.txt (line 60))
  Using cached MarkupSafe-3.0.2-cp39-cp39-macosx_10_9_universal2.whl.metadata (4.0 kB)
Collecting matplotlib==3.9.3 (from -r requirements-freeze.txt (line 61))
  Using cached matplotlib-3.9.3-cp39-cp39-macosx_10_12_x86_64.whl.metadata (11 kB)
Collecting matplotlib-inline==0.1.7 (from -r requirements-freeze.txt (line 62))
  Using cached matplotlib_inline-0.1.7-py3-none-any.whl.metadata (3.9 kB)
Collecting mdurl==0.1.2 (from -r requirements-freeze.txt (line 63))
  Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
Collecting monai==1.4.0 (from -r requirements-freeze.txt (line 64))
  Using cached monai-1.4.0-py3-none-any.whl.metadata (11 kB)
Collecting mpmath==1.3.0 (from -r requirements-freeze.txt (line 65))
  Using cached https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl (536 kB)
Collecting networkx==3.2.1 (from -r requirements-freeze.txt (line 66))
  Using cached https://download.pytorch.org/whl/networkx-3.2.1-py3-none-any.whl (1.6 MB)
Collecting neurite==0.2 (from -r requirements-freeze.txt (line 67))
  Using cached neurite-0.2-py3-none-any.whl.metadata (653 bytes)
Collecting nibabel==5.3.2 (from -r requirements-freeze.txt (line 68))
  Using cached nibabel-5.3.2-py3-none-any.whl.metadata (9.1 kB)
Collecting nilearn==0.10.4 (from -r requirements-freeze.txt (line 69))
  Using cached nilearn-0.10.4-py3-none-any.whl.metadata (7.8 kB)
Collecting nnunetv2==2.3.1 (from -r requirements-freeze.txt (line 70))
  Using cached nnunetv2-2.3.1-py3-none-any.whl
Collecting num2words==0.5.13 (from -r requirements-freeze.txt (line 71))
  Using cached num2words-0.5.13-py3-none-any.whl.metadata (12 kB)
Collecting numpy==1.26.4 (from -r requirements-freeze.txt (line 72))
  Using cached numpy-1.26.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (61 kB)
Collecting onnx==1.17.0 (from -r requirements-freeze.txt (line 73))
  Using cached onnx-1.17.0-cp39-cp39-macosx_12_0_universal2.whl.metadata (16 kB)
Collecting onnxruntime==1.19.2 (from -r requirements-freeze.txt (line 74))
  Using cached onnxruntime-1.19.2-cp39-cp39-macosx_11_0_universal2.whl.metadata (4.5 kB)
Collecting orderly-set==5.2.2 (from -r requirements-freeze.txt (line 75))
  Using cached orderly_set-5.2.2-py3-none-any.whl.metadata (6.3 kB)
Collecting packaging==24.2 (from -r requirements-freeze.txt (line 76))
  Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pandas==1.5.3 (from -r requirements-freeze.txt (line 77))
  Using cached pandas-1.5.3-cp39-cp39-macosx_10_9_x86_64.whl.metadata (11 kB)
Collecting pillow==11.0.0 (from -r requirements-freeze.txt (line 78))
  Using cached https://download.pytorch.org/whl/pillow-11.0.0-cp39-cp39-macosx_10_10_x86_64.whl.metadata (9.1 kB)
Collecting platformdirs==4.3.6 (from -r requirements-freeze.txt (line 79))
  Using cached platformdirs-4.3.6-py3-none-any.whl.metadata (11 kB)
Collecting pluggy==1.5.0 (from -r requirements-freeze.txt (line 80))
  Using cached pluggy-1.5.0-py3-none-any.whl.metadata (4.8 kB)
Collecting portalocker==3.0.0 (from -r requirements-freeze.txt (line 81))
  Using cached portalocker-3.0.0-py3-none-any.whl.metadata (8.5 kB)
Collecting protobuf==5.29.0 (from -r requirements-freeze.txt (line 82))
  Using cached protobuf-5.29.0-cp38-abi3-macosx_10_9_universal2.whl.metadata (592 bytes)
Collecting psutil==6.1.0 (from -r requirements-freeze.txt (line 83))
  Using cached psutil-6.1.0-cp36-abi3-macosx_10_9_x86_64.whl.metadata (22 kB)
Collecting pybids==0.15.5 (from -r requirements-freeze.txt (line 84))
  Using cached pybids-0.15.5-py3-none-any.whl.metadata (3.2 kB)
Collecting pydicom==2.4.4 (from -r requirements-freeze.txt (line 85))
  Using cached pydicom-2.4.4-py3-none-any.whl.metadata (7.8 kB)
Collecting Pygments==2.18.0 (from -r requirements-freeze.txt (line 86))
  Using cached pygments-2.18.0-py3-none-any.whl.metadata (2.5 kB)
Collecting pyparsing==3.2.0 (from -r requirements-freeze.txt (line 87))
  Using cached pyparsing-3.2.0-py3-none-any.whl.metadata (5.0 kB)
Collecting PyQt5==5.12.3 (from -r requirements-freeze.txt (line 88))
  Using cached PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-macosx_10_6_intel.whl.metadata (2.2 kB)
Collecting PyQt5-sip==12.12.2 (from -r requirements-freeze.txt (line 89))
  Using cached PyQt5_sip-12.12.2-cp39-cp39-macosx_10_9_universal2.whl.metadata (504 bytes)
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Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
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Using cached zipp-3.21.0-py3-none-any.whl (9.6 kB)
Using cached setuptools-75.8.0-py3-none-any.whl (1.2 MB)
Using cached torchio-0.20.4-py3-none-any.whl (175 kB)
Using cached argparse-1.4.0-py2.py3-none-any.whl (23 kB)
Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, argparse, zipp, XlsxWriter, wrapt, urllib3, typing_extensions, types-setuptools, traitlets, traceback2, tqdm, tomli, threadpoolctl, tensorboard-data-server, sympy, SQLAlchemy, smmap, six, shellingham, setuptools, setproctitle, rpds-py, PyYAML, python-gdcm, PyQt5-sip, pyparsing, Pygments, pydicom, psutil, protobuf, portalocker, pluggy, platformdirs, pillow, packaging, orderly-set, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, Cython, cycler, coverage, click, charset-normalizer, certifi, attrs, astor, absl-py, yacs, wquantiles, Werkzeug, unittest2, transforms3d, tifffile, setuptools-scm, sentry-sdk, scipy, requirements-parser, requests, referencing, python-dateutil, pytest, PyQt5, onnx, matplotlib-inline, markdown-it-py, lazy_loader, Jinja2, importlib_resources, importlib_metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, deepdiff, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest-console-scripts, pandas, onnxruntime, nibabel, matplotlib, Markdown, jsonschema-specifications, gryds, GitPython, wandb, typer, trx-python, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, jsonschema, formulaic, dynamic_network_architectures, dicom2nifti, batchgenerators, torchio, neurite, dipy, bidsschematools, acvl_utils, voxelmorph, nnunetv2, bids-validator, totalspineseg, pybids, ivadomed
Successfully installed Cython-3.0.11 Deprecated-1.2.15 GitPython-3.1.43 Jinja2-3.1.4 Markdown-3.7 MarkupSafe-3.0.2 PyQt5-5.12.3 PyQt5-sip-12.12.2 PyYAML-6.0.2 Pygments-2.18.0 SQLAlchemy-1.3.24 SimpleITK-2.4.0 Werkzeug-3.1.3 XlsxWriter-3.2.0 absl-py-2.1.0 acvl_utils-0.2 argparse-1.4.0 astor-0.8.1 attrs-24.2.0 batchgenerators-0.25.1 bids-validator-1.14.7.post0 bidsschematools-0.11.3.post3 certifi-2024.8.30 charset-normalizer-3.4.0 click-8.1.7 coloredlogs-15.0.1 connected-components-3d-3.21.0 contourpy-1.3.0 coverage-7.6.8 csv-diff-1.2 cycler-0.12.1 deepdiff-8.0.1 dicom2nifti-2.5.0 dictdiffer-0.9.0 dipy-1.8.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic_network_architectures-0.3.1 exceptiongroup-1.2.2 filelock-3.16.1 flatbuffers-24.3.25 fonttools-4.55.1 formulaic-0.3.4 fsspec-2024.10.0 future-1.0.0 gitdb-4.0.11 graphviz-0.20.3 grpcio-1.68.1 gryds-0.0.9 h5py-3.12.1 humanfriendly-10.0 humanize-4.11.0 idna-3.10 imagecodecs-2024.9.22 imageio-2.36.1 importlib_metadata-8.5.0 importlib_resources-6.4.5 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.10 joblib-1.4.2 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 kiwisolver-1.4.7 lazy_loader-0.4 linecache2-1.0.0 loguru-0.7.2 lxml-5.3.0 markdown-it-py-3.0.0 matplotlib-3.9.3 matplotlib-inline-0.1.7 mdurl-0.1.2 monai-1.4.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-5.3.2 nilearn-0.10.4 nnunetv2-2.3.1 num2words-0.5.13 numpy-1.26.4 onnx-1.17.0 onnxruntime-1.19.2 orderly-set-5.2.2 packaging-24.2 pandas-1.5.3 pillow-11.0.0 platformdirs-4.3.6 pluggy-1.5.0 portalocker-3.0.0 protobuf-5.29.0 psutil-6.1.0 pybids-0.15.5 pydicom-2.4.4 pyparsing-3.2.0 pystrum-0.4 pytest-8.3.4 pytest-console-scripts-1.4.1 pytest-cov-6.0.0 python-dateutil-2.9.0.post0 python-gdcm-3.0.24.1 pytz-2024.2 referencing-0.35.1 requests-2.32.3 requirements-parser-0.11.0 rich-13.9.4 rpds-py-0.22.1 scikit-image-0.24.0 scikit-learn-1.5.2 scipy-1.13.1 seaborn-0.13.2 sentry-sdk-2.19.0 setproctitle-1.3.4 setuptools-75.8.0 setuptools-scm-8.1.0 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sympy-1.13.1 tensorboard-2.18.0 tensorboard-data-server-0.7.2 threadpoolctl-3.5.0 tifffile-2024.8.30 tomli-2.2.1 torch-2.2.2 torchio-0.20.4 torchvision-0.17.2 totalspineseg-20241128 tqdm-4.67.1 traceback2-1.4.0 traitlets-5.14.3 transforms3d-0.4.2 trx-python-0.3 typer-0.15.0 types-setuptools-75.6.0.20241126 typing_extensions-4.12.2 unittest2-1.1.0 urllib3-2.2.3 voxelmorph-0.2 wandb-0.18.7 wquantiles-0.6 wrapt-1.17.0 xlwt-1.3.0 yacs-0.1.8 zipp-3.21.0

Installing spinalcordtoolbox...

Obtaining file:///Users/dominicvhoule/sct_6.5
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Checking if build backend supports build_editable: started
  Checking if build backend supports build_editable: finished with status 'done'
  Getting requirements to build editable: started
  Getting requirements to build editable: finished with status 'done'
  Preparing editable metadata (pyproject.toml): started
  Preparing editable metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: spinalcordtoolbox
  Building editable for spinalcordtoolbox (pyproject.toml): started
  Building editable for spinalcordtoolbox (pyproject.toml): finished with status 'done'
  Created wheel for spinalcordtoolbox: filename=spinalcordtoolbox-6.5-0.editable-py3-none-any.whl size=9744 sha256=b5e25c731a4448bad67fbd9fd7d8ea85abfa61bf7be754ca37e36710ab8341ee
  Stored in directory: /private/var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/pip-ephem-wheel-cache-bxldme5_/wheels/7c/ac/a3/0ccf3961fb554dfd2a99e5e5969d0d232484d88cff0379141d
Successfully built spinalcordtoolbox
Installing collected packages: spinalcordtoolbox
Successfully installed spinalcordtoolbox-6.5

Creating launchers for Python scripts...


Installing binaries...


sct_download_data -d binaries_osx -k


--
Spinal Cord Toolbox (6.5)

sct_download_data -d binaries_osx -k
--

Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221018/spinalcordtoolbox-binaries_osx.tar.gz
Downloading: spinalcordtoolbox-binaries_osx.tar.gz

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Creating temporary folder (/var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/sct_2025-02-11_13-07-48_install-data_x4hd0ipf)
Unzip data to: /var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/sct_2025-02-11_13-07-48_install-data_x4hd0ipf
Copying data to: /Users/dominicvhoule/sct_6.5/bin
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Removing temporary folders...
Done!


All requirements installed!


Installing data...


mkdir -p /Users/dominicvhoule/sct_6.5/data


sct_download_data -d default -k


--
Spinal Cord Toolbox (6.5)

sct_download_data -d default -k
--

Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20240215/PAM50-r20240215.zip
Downloading: PAM50-r20240215.zip

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Creating temporary folder (/var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/sct_2025-02-11_13-07-53_install-data_yiz4nffj)
Unzip data to: /var/folders/_c/vzc_02w12kgfdyx421bnrr2r0000gn/T/sct_2025-02-11_13-07-53_install-data_yiz4nffj
Copying data to: /Users/dominicvhoule/sct_6.5/data/PAM50
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install_sct-6.5_macos.sh: line 288: /Users/dominicvhoule/.zshrc: Permission denied

Installation failed!

Please find the file "/Users/dominicvhoule/sct_6.5/install_sct_log.txt",
then upload it as a .txt attachment in a new topic on SCT's forum:
--> https://forum.spinalcordmri.org/c/sct