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

Darwin Davids-MacBook-Pro-2.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64
ProductVersion:	10.13.6

Checking requirements...


OK!


SCT version ......... 6.4
Installation type ... package
Operating system .... osx (10.13.6)
Shell config ........ /Users/davidwarrenmartin/.bashrc

SCT will be installed here: [/Users/davidwarrenmartin/sct_6.4]



Do you agree? [y]es/[n]o: 
Copying source files from /Users/davidwarrenmartin/Desktop/Research/CSF_Flow/Spinal_Cord_Toolbox/spinalcordtoolbox-6.4 to /Users/davidwarrenmartin/sct_6.4

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


curl -sS -o /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/tmp.Qm83pfJN/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh


Installing Miniconda...


bash /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/tmp.Qm83pfJN/miniconda.sh -p /Users/davidwarrenmartin/sct_6.4/python -b -f

PREFIX=/Users/davidwarrenmartin/sct_6.4/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/davidwarrenmartin/sct_6.4/python/envs/venv_sct

  added / updated specs:
    - python=3.9


The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2024.7.2-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-24.2-py39hecd8cb5_0 
  python             pkgs/main/osx-64::python-3.9.19-h5ee71fb_1 
  readline           pkgs/main/osx-64::readline-8.2-hca72f7f_0 
  setuptools         pkgs/main/osx-64::setuptools-72.1.0-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-2024a-h04d1e81_0 
  wheel              pkgs/main/osx-64::wheel-0.44.0-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... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate /Users/davidwarrenmartin/sct_6.4/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 (24.2)

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-2024.8.30-py3-none-any.whl.metadata (2.2 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.tar.gz (18 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
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 (from -r requirements-freeze.txt (line 5))
  Using cached batchgenerators-0.25.tar.gz (61 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
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==0.10.0 (from -r requirements-freeze.txt (line 7))
  Using cached bidsschematools-0.10.0-py3-none-any.whl.metadata (3.6 kB)
Collecting certifi
  Using cached certifi-2024.7.4-py3-none-any.whl.metadata (2.2 kB)
Collecting charset-normalizer==3.3.2 (from -r requirements-freeze.txt (line 9))
  Using cached charset_normalizer-3.3.2-cp39-cp39-macosx_10_9_x86_64.whl.metadata (33 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==3.18.0 (from -r requirements-freeze.txt (line 12))
  Using cached connected_components_3d-3.18.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (31 kB)
Collecting contourpy==1.2.1 (from -r requirements-freeze.txt (line 13))
  Using cached contourpy-1.2.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (5.8 kB)
Collecting coverage==7.6.1 (from -r requirements-freeze.txt (line 14))
  Using cached coverage-7.6.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (8.3 kB)
Collecting csv-diff==1.1 (from -r requirements-freeze.txt (line 15))
  Using cached csv_diff-1.1-py3-none-any.whl.metadata (4.1 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==7.0.1 (from -r requirements-freeze.txt (line 18))
  Using cached deepdiff-7.0.1-py3-none-any.whl.metadata (6.8 kB)
Collecting Deprecated==1.2.14 (from -r requirements-freeze.txt (line 19))
  Using cached Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)
Collecting dicom2nifti==2.4.11 (from -r requirements-freeze.txt (line 20))
  Using cached dicom2nifti-2.4.11-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.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting dynamic_network_architectures==0.3.1 (from -r requirements-freeze.txt (line 25))
  Using cached dynamic_network_architectures-0.3.1.tar.gz (20 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
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==3.15.4 (from -r requirements-freeze.txt (line 27))
  Using cached filelock-3.15.4-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==4.53.1 (from -r requirements-freeze.txt (line 29))
  Using cached fonttools-4.53.1-cp39-cp39-macosx_10_9_universal2.whl.metadata (162 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==2024.6.1 (from -r requirements-freeze.txt (line 31))
  Using cached fsspec-2024.6.1-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==1.65.4 (from -r requirements-freeze.txt (line 36))
  Using cached grpcio-1.65.4-cp39-cp39-macosx_10_9_universal2.whl.metadata (3.3 kB)
Collecting h5py==3.11.0 (from -r requirements-freeze.txt (line 37))
  Using cached h5py-3.11.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.5 kB)
Collecting humanfriendly==10.0 (from -r requirements-freeze.txt (line 38))
  Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB)
Collecting humanize==4.10.0 (from -r requirements-freeze.txt (line 39))
  Using cached humanize-4.10.0-py3-none-any.whl.metadata (7.9 kB)
Collecting idna==3.7 (from -r requirements-freeze.txt (line 40))
  Using cached idna-3.7-py3-none-any.whl.metadata (9.9 kB)
Collecting imagecodecs==2024.6.1 (from -r requirements-freeze.txt (line 41))
  Using cached imagecodecs-2024.6.1.tar.gz (9.5 MB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting imageio==2.34.2 (from -r requirements-freeze.txt (line 42))
  Using cached imageio-2.34.2-py3-none-any.whl.metadata (4.9 kB)
Collecting importlib_metadata==8.2.0 (from -r requirements-freeze.txt (line 43))
  Using cached importlib_metadata-8.2.0-py3-none-any.whl.metadata (4.7 kB)
Collecting importlib_resources==6.4.0 (from -r requirements-freeze.txt (line 44))
  Using cached importlib_resources-6.4.0-py3-none-any.whl.metadata (3.9 kB)
Collecting iniconfig==2.0.0 (from -r requirements-freeze.txt (line 45))
  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 46))
  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 47))
  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 48))
  Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
Collecting joblib==1.4.2 (from -r requirements-freeze.txt (line 49))
  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 50))
  Using cached jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB)
Collecting jsonschema-specifications==2023.12.1 (from -r requirements-freeze.txt (line 51))
  Using cached jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB)
Collecting kiwisolver==1.4.5 (from -r requirements-freeze.txt (line 52))
  Using cached kiwisolver-1.4.5-cp39-cp39-macosx_10_9_x86_64.whl.metadata (6.4 kB)
Collecting lazy_loader==0.4 (from -r requirements-freeze.txt (line 53))
  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 54))
  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 55))
  Using cached loguru-0.7.2-py3-none-any.whl.metadata (23 kB)
Collecting lxml==5.2.2 (from -r requirements-freeze.txt (line 56))
  Using cached lxml-5.2.2-cp39-cp39-macosx_10_9_x86_64.whl.metadata (3.4 kB)
Collecting Markdown==3.6 (from -r requirements-freeze.txt (line 57))
  Using cached Markdown-3.6-py3-none-any.whl.metadata (7.0 kB)
Collecting markdown-it-py==3.0.0 (from -r requirements-freeze.txt (line 58))
  Using cached markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting MarkupSafe==2.1.5 (from -r requirements-freeze.txt (line 59))
  Using cached https://download.pytorch.org/whl/MarkupSafe-2.1.5-cp39-cp39-macosx_10_9_x86_64.whl (14 kB)
Collecting matplotlib==3.9.1.post1 (from -r requirements-freeze.txt (line 60))
  Using cached matplotlib-3.9.1.post1-cp39-cp39-macosx_10_12_x86_64.whl.metadata (11 kB)
Collecting matplotlib-inline==0.1.7 (from -r requirements-freeze.txt (line 61))
  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 62))
  Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
Collecting monai==1.3.2 (from -r requirements-freeze.txt (line 63))
  Using cached monai-1.3.2-py3-none-any.whl.metadata (10 kB)
Collecting mpmath==1.3.0 (from -r requirements-freeze.txt (line 64))
  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 65))
  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 66))
  Using cached neurite-0.2-py3-none-any.whl.metadata (653 bytes)
Collecting nibabel==5.2.1 (from -r requirements-freeze.txt (line 67))
  Using cached nibabel-5.2.1-py3-none-any.whl.metadata (8.8 kB)
Collecting nilearn==0.10.4 (from -r requirements-freeze.txt (line 68))
  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 69))
  Using cached nnunetv2-2.3.1.tar.gz (182 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting num2words==0.5.13 (from -r requirements-freeze.txt (line 70))
  Using cached num2words-0.5.13-py3-none-any.whl.metadata (12 kB)
Collecting numpy==1.26.4 (from -r requirements-freeze.txt (line 71))
  Using cached numpy-1.26.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (61 kB)
Collecting onnx==1.16.2 (from -r requirements-freeze.txt (line 72))
  Using cached onnx-1.16.2.tar.gz (12.3 MB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
ERROR: Ignored the following versions that require a different python version: 2.1.0 Requires-Python >=3.10; 2.1.0rc1 Requires-Python >=3.10; 2.1.1 Requires-Python >=3.10; 2.5.2 Requires-Python !=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,<3.9dev,>=2.7; 2.7.0 Requires-Python >=3.6, <3.9; 2.7.1 Requires-Python >=3.6, <3.9; 2.7.2 Requires-Python >=3.6, <3.9; 2.7.4 Requires-Python >=3.6, <3.9; 2.8.0 Requires-Python >=3.6, <3.9; 3.3 Requires-Python >=3.10; 3.3rc0 Requires-Python >=3.10
ERROR: Could not find a version that satisfies the requirement onnxruntime==1.18.1 (from versions: 1.7.0, 1.8.0, 1.8.1)
ERROR: No matching distribution found for onnxruntime==1.18.1

Failed running pip install: 1


Installation failed!

Please find the file "/Users/davidwarrenmartin/sct_6.4/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