*******************************
* Welcome to SCT installation *
*******************************



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 ......... 5.6
Installation type ... package
Operating system .... osx (10.13.6)
Shell config ........ /Users/davidwarrenmartin/.bashrc

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: 
--> Crash reports will be sent to the SCT development team. Thank you!


SCT will be installed here: [/Users/davidwarrenmartin/sct_5.6]



Do you agree? [y]es/[n]o: 
Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: 
Copying source files from /Users/davidwarrenmartin/Desktop/Research/CSF_Flow/Spinal_Cord_Toolbox/spinalcordtoolbox-5.6 to /Users/davidwarrenmartin/sct_5.6

..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
rm -rf /Users/davidwarrenmartin/sct_5.6/python


mkdir -p /Users/davidwarrenmartin/sct_5.6/python


Downloading Miniconda...


curl -sS -o /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/tmp.a91FbvMi/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh


Installing Miniconda...


bash /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/tmp.a91FbvMi/miniconda.sh -p /Users/davidwarrenmartin/sct_5.6/python -b -f

PREFIX=/Users/davidwarrenmartin/sct_5.6/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_5.6/python/envs/venv_sct

  added / updated specs:
    - python=3.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2022.12.7          |   py37hecd8cb5_0         151 KB
    openssl-1.1.1w             |       hca72f7f_0         2.8 MB
    pip-22.3.1                 |   py37hecd8cb5_0         2.7 MB
    python-3.7.16              |       h218abb5_0        23.5 MB
    setuptools-65.6.3          |   py37hecd8cb5_0         1.1 MB
    wheel-0.38.4               |   py37hecd8cb5_0          65 KB
    ------------------------------------------------------------
                                           Total:        30.4 MB

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2024.7.2-hecd8cb5_0 
  certifi            pkgs/main/osx-64::certifi-2022.12.7-py37hecd8cb5_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-1.1.1w-hca72f7f_0 
  pip                pkgs/main/osx-64::pip-22.3.1-py37hecd8cb5_0 
  python             pkgs/main/osx-64::python-3.7.16-h218abb5_0 
  readline           pkgs/main/osx-64::readline-8.2-hca72f7f_0 
  setuptools         pkgs/main/osx-64::setuptools-65.6.3-py37hecd8cb5_0 
  sqlite             pkgs/main/osx-64::sqlite-3.45.3-h6c40b1e_0 
  tk                 pkgs/main/osx-64::tk-8.6.14-h4d00af3_0 
  wheel              pkgs/main/osx-64::wheel-0.38.4-py37hecd8cb5_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 venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate


Validating that conda environment can be activated...

Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.7/site-packages (22.3.1)
Collecting pip!=21.2.*
  Using cached pip-24.0-py3-none-any.whl (2.1 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 22.3.1
    Uninstalling pip-22.3.1:
      Successfully uninstalled pip-22.3.1
Successfully installed pip-24.0

Installing Python dependencies...


Using requirements-freeze.txt (release installation)

Looking in links: https://download.pytorch.org/whl/torch/, https://download.pytorch.org/whl/torchvision/
Ignoring torch: markers 'sys_platform != "darwin"' don't match your environment
Ignoring torchvision: markers 'sys_platform != "darwin"' don't match your environment
Collecting certifi
  Using cached certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
Collecting absl-py==1.0.0 (from -r requirements-freeze.txt (line 1))
  Using cached absl_py-1.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting astor==0.7.1 (from -r requirements-freeze.txt (line 2))
  Using cached astor-0.7.1-py2.py3-none-any.whl.metadata (4.3 kB)
Collecting attrs==21.4.0 (from -r requirements-freeze.txt (line 3))
  Using cached attrs-21.4.0-py2.py3-none-any.whl.metadata (9.8 kB)
Collecting bids-validator==1.9.3 (from -r requirements-freeze.txt (line 4))
  Using cached bids_validator-1.9.3-py2.py3-none-any.whl.metadata (38 kB)
Collecting certifi
  Using cached certifi-2021.10.8-py2.py3-none-any.whl.metadata (3.0 kB)
Collecting cffi==1.15.0 (from -r requirements-freeze.txt (line 6))
  Using cached cffi-1.15.0-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (1.2 kB)
Collecting charset-normalizer==2.0.12 (from -r requirements-freeze.txt (line 7))
  Using cached charset_normalizer-2.0.12-py3-none-any.whl.metadata (11 kB)
Collecting click==8.1.3 (from -r requirements-freeze.txt (line 8))
  Using cached click-8.1.3-py3-none-any.whl.metadata (3.2 kB)
Collecting coverage==6.3.2 (from -r requirements-freeze.txt (line 9))
  Using cached coverage-6.3.2-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (7.7 kB)
Collecting cryptography==37.0.1 (from -r requirements-freeze.txt (line 10))
  Using cached cryptography-37.0.1-cp36-abi3-macosx_10_10_x86_64.whl.metadata (5.5 kB)
Collecting csv-diff==1.1 (from -r requirements-freeze.txt (line 11))
  Using cached csv_diff-1.1-py3-none-any.whl.metadata (4.1 kB)
Collecting cycler==0.11.0 (from -r requirements-freeze.txt (line 12))
  Using cached cycler-0.11.0-py3-none-any.whl.metadata (785 bytes)
Collecting Deprecated==1.2.13 (from -r requirements-freeze.txt (line 13))
  Using cached Deprecated-1.2.13-py2.py3-none-any.whl.metadata (5.8 kB)
Collecting dictdiffer==0.9.0 (from -r requirements-freeze.txt (line 14))
  Using cached dictdiffer-0.9.0-py2.py3-none-any.whl.metadata (4.8 kB)
Collecting dipy==1.5.0 (from -r requirements-freeze.txt (line 15))
  Using cached dipy-1.5.0-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (3.9 kB)
Collecting docopt==0.6.2 (from -r requirements-freeze.txt (line 16))
  Using cached docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting fonttools==4.33.3 (from -r requirements-freeze.txt (line 17))
  Using cached fonttools-4.33.3-py3-none-any.whl.metadata (125 kB)
Collecting formulaic==0.3.3 (from -r requirements-freeze.txt (line 18))
  Using cached formulaic-0.3.3-py3-none-any.whl.metadata (5.6 kB)
Collecting future==0.18.2 (from -r requirements-freeze.txt (line 19))
  Using cached future-0.18.2.tar.gz (829 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting gast==0.2.2 (from -r requirements-freeze.txt (line 20))
  Using cached gast-0.2.2.tar.gz (10 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting google-pasta==0.2.0 (from -r requirements-freeze.txt (line 21))
  Using cached google_pasta-0.2.0-py3-none-any.whl.metadata (814 bytes)
Collecting grpcio==1.44.0 (from -r requirements-freeze.txt (line 22))
  Using cached grpcio-1.44.0-cp37-cp37m-macosx_10_10_x86_64.whl.metadata (4.0 kB)
Collecting h5py==2.10.0 (from -r requirements-freeze.txt (line 23))
  Using cached h5py-2.10.0-cp37-cp37m-macosx_10_6_intel.whl.metadata (2.0 kB)
Collecting humanize==4.0.0 (from -r requirements-freeze.txt (line 24))
  Using cached humanize-4.0.0-py3-none-any.whl.metadata (7.5 kB)
Collecting idna==3.3 (from -r requirements-freeze.txt (line 25))
  Using cached idna-3.3-py3-none-any.whl.metadata (9.8 kB)
Collecting imageio==2.18.0 (from -r requirements-freeze.txt (line 26))
  Using cached imageio-2.18.0-py3-none-any.whl.metadata (4.8 kB)
Collecting importlib-metadata==4.11.3 (from -r requirements-freeze.txt (line 27))
  Using cached importlib_metadata-4.11.3-py3-none-any.whl.metadata (4.0 kB)
Collecting iniconfig==1.1.1 (from -r requirements-freeze.txt (line 28))
  Using cached iniconfig-1.1.1-py2.py3-none-any.whl.metadata (2.4 kB)
Collecting interface-meta==1.3.0 (from -r requirements-freeze.txt (line 29))
  Using cached interface_meta-1.3.0-py3-none-any.whl.metadata (6.7 kB)
Collecting ivadomed==2.9.5 (from -r requirements-freeze.txt (line 30))
  Using cached ivadomed-2.9.5-py3-none-any.whl.metadata (4.4 kB)
Collecting joblib==1.1.0 (from -r requirements-freeze.txt (line 31))
  Using cached joblib-1.1.0-py2.py3-none-any.whl.metadata (5.2 kB)
Collecting Keras==2.3.1 (from -r requirements-freeze.txt (line 32))
  Using cached Keras-2.3.1-py2.py3-none-any.whl.metadata (2.2 kB)
Collecting Keras-Applications==1.0.8 (from -r requirements-freeze.txt (line 33))
  Using cached Keras_Applications-1.0.8-py3-none-any.whl.metadata (1.7 kB)
Collecting Keras-Preprocessing==1.1.2 (from -r requirements-freeze.txt (line 34))
  Using cached Keras_Preprocessing-1.1.2-py2.py3-none-any.whl.metadata (1.9 kB)
Collecting kiwisolver==1.4.2 (from -r requirements-freeze.txt (line 35))
  Using cached kiwisolver-1.4.2-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (6.4 kB)
Collecting loguru==0.6.0 (from -r requirements-freeze.txt (line 36))
  Using cached loguru-0.6.0-py3-none-any.whl.metadata (21 kB)
Collecting Markdown==3.3.6 (from -r requirements-freeze.txt (line 37))
  Using cached Markdown-3.3.6-py3-none-any.whl.metadata (4.6 kB)
Collecting matplotlib==3.5.1 (from -r requirements-freeze.txt (line 38))
  Using cached matplotlib-3.5.1-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (6.7 kB)
Collecting networkx==2.6.3 (from -r requirements-freeze.txt (line 39))
  Using cached networkx-2.6.3-py3-none-any.whl.metadata (5.0 kB)
Collecting nibabel==3.2.2 (from -r requirements-freeze.txt (line 40))
  Using cached nibabel-3.2.2-py3-none-any.whl.metadata (6.2 kB)
Collecting num2words==0.5.10 (from -r requirements-freeze.txt (line 41))
  Using cached num2words-0.5.10-py3-none-any.whl.metadata (8.9 kB)
Collecting numpy==1.18.5 (from -r requirements-freeze.txt (line 42))
  Using cached numpy-1.18.5-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (2.1 kB)
Collecting onnxruntime==1.7.0 (from -r requirements-freeze.txt (line 43))
  Using cached onnxruntime-1.7.0-cp37-cp37m-macosx_10_12_x86_64.whl.metadata (2.9 kB)
Collecting opt-einsum==3.3.0 (from -r requirements-freeze.txt (line 44))
  Using cached opt_einsum-3.3.0-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging==21.3 (from -r requirements-freeze.txt (line 45))
  Using cached packaging-21.3-py3-none-any.whl.metadata (15 kB)
Collecting pandas==1.3.5 (from -r requirements-freeze.txt (line 46))
  Using cached pandas-1.3.5-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (12 kB)
Collecting Pillow==9.1.0 (from -r requirements-freeze.txt (line 47))
  Using cached Pillow-9.1.0-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (8.7 kB)
Collecting pluggy==1.0.0 (from -r requirements-freeze.txt (line 48))
  Using cached pluggy-1.0.0-py2.py3-none-any.whl.metadata (4.3 kB)
Collecting portalocker==2.4.0 (from -r requirements-freeze.txt (line 49))
  Using cached portalocker-2.4.0-py2.py3-none-any.whl.metadata (6.8 kB)
Collecting protobuf==3.20.1 (from -r requirements-freeze.txt (line 50))
  Using cached protobuf-3.20.1-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (698 bytes)
Collecting psutil==5.9.0 (from -r requirements-freeze.txt (line 51))
  Using cached psutil-5.9.0-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (21 kB)
Collecting py==1.11.0 (from -r requirements-freeze.txt (line 52))
  Using cached py-1.11.0-py2.py3-none-any.whl.metadata (2.8 kB)
Collecting pybids==0.15.1 (from -r requirements-freeze.txt (line 53))
  Using cached pybids-0.15.1-py3-none-any.whl.metadata (2.4 kB)
Collecting pycparser==2.21 (from -r requirements-freeze.txt (line 54))
  Using cached pycparser-2.21-py2.py3-none-any.whl.metadata (1.1 kB)
Collecting pyOpenSSL==22.0.0 (from -r requirements-freeze.txt (line 55))
  Using cached pyOpenSSL-22.0.0-py2.py3-none-any.whl.metadata (7.8 kB)
Collecting pyparsing==2.4.7 (from -r requirements-freeze.txt (line 56))
  Using cached pyparsing-2.4.7-py2.py3-none-any.whl.metadata (3.6 kB)
Collecting PyQt5==5.11.3 (from -r requirements-freeze.txt (line 57))
  Using cached PyQt5-5.11.3-5.11.2_a-cp35.cp36.cp37.cp38-abi3-macosx_10_6_intel.whl.metadata (2.2 kB)
Collecting PyQt5_sip==4.19.19 (from -r requirements-freeze.txt (line 58))
  Using cached PyQt5_sip-4.19.19-cp37-cp37m-macosx_10_6_intel.whl.metadata (2.8 kB)
Collecting pytest==7.1.2 (from -r requirements-freeze.txt (line 59))
  Using cached pytest-7.1.2-py3-none-any.whl.metadata (7.8 kB)
Collecting pytest-console-scripts==1.3.1 (from -r requirements-freeze.txt (line 60))
  Using cached pytest_console_scripts-1.3.1-py3-none-any.whl.metadata (9.7 kB)
Collecting pytest-cov==3.0.0 (from -r requirements-freeze.txt (line 61))
  Using cached pytest_cov-3.0.0-py3-none-any.whl.metadata (24 kB)
Collecting python-dateutil==2.8.2 (from -r requirements-freeze.txt (line 62))
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting pytz==2022.1 (from -r requirements-freeze.txt (line 63))
  Using cached pytz-2022.1-py2.py3-none-any.whl.metadata (21 kB)
Collecting PyWavelets==1.3.0 (from -r requirements-freeze.txt (line 64))
  Using cached PyWavelets-1.3.0-cp37-cp37m-macosx_10_13_x86_64.whl.metadata (1.9 kB)
Collecting PyYAML==6.0 (from -r requirements-freeze.txt (line 65))
  Using cached PyYAML-6.0-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (2.0 kB)
Collecting raven==6.10.0 (from -r requirements-freeze.txt (line 66))
  Using cached raven-6.10.0-py2.py3-none-any.whl.metadata (2.9 kB)
Collecting requests==2.27.1 (from -r requirements-freeze.txt (line 67))
  Using cached requests-2.27.1-py2.py3-none-any.whl.metadata (5.0 kB)
Collecting requirements-parser==0.5.0 (from -r requirements-freeze.txt (line 68))
  Using cached requirements_parser-0.5.0-py3-none-any.whl.metadata (3.1 kB)
Collecting scikit-image==0.19.2 (from -r requirements-freeze.txt (line 69))
  Using cached scikit_image-0.19.2-cp37-cp37m-macosx_10_13_x86_64.whl.metadata (8.0 kB)
Collecting scikit-learn==1.0.2 (from -r requirements-freeze.txt (line 70))
  Using cached scikit_learn-1.0.2-cp37-cp37m-macosx_10_13_x86_64.whl.metadata (10 kB)
Collecting scipy==1.7.3 (from -r requirements-freeze.txt (line 71))
  Using cached scipy-1.7.3-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (2.2 kB)
Collecting seaborn==0.11.2 (from -r requirements-freeze.txt (line 72))
  Using cached seaborn-0.11.2-py3-none-any.whl.metadata (2.3 kB)
Collecting SimpleITK==2.1.1.2 (from -r requirements-freeze.txt (line 73))
  Using cached SimpleITK-2.1.1.2-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (8.1 kB)
Collecting six==1.16.0 (from -r requirements-freeze.txt (line 74))
  Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting SQLAlchemy==1.3.24 (from -r requirements-freeze.txt (line 75))
  Using cached SQLAlchemy-1.3.24.tar.gz (6.4 MB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting tensorboard==1.15.0 (from -r requirements-freeze.txt (line 76))
  Using cached tensorboard-1.15.0-py3-none-any.whl.metadata (1.8 kB)
Collecting tensorflow==1.15.5 (from -r requirements-freeze.txt (line 77))
  Using cached tensorflow-1.15.5-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (2.8 kB)
Collecting tensorflow-estimator==1.15.1 (from -r requirements-freeze.txt (line 78))
  Using cached tensorflow_estimator-1.15.1-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting termcolor==1.1.0 (from -r requirements-freeze.txt (line 79))
  Using cached termcolor-1.1.0.tar.gz (3.9 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting threadpoolctl==3.1.0 (from -r requirements-freeze.txt (line 80))
  Using cached threadpoolctl-3.1.0-py3-none-any.whl.metadata (9.2 kB)
Collecting tifffile==2021.11.2 (from -r requirements-freeze.txt (line 81))
  Using cached tifffile-2021.11.2-py3-none-any.whl.metadata (29 kB)
Collecting tomli==2.0.1 (from -r requirements-freeze.txt (line 82))
  Using cached tomli-2.0.1-py3-none-any.whl.metadata (8.9 kB)
Collecting tqdm==4.64.0 (from -r requirements-freeze.txt (line 83))
  Using cached tqdm-4.64.0-py2.py3-none-any.whl.metadata (57 kB)
Collecting transforms3d==0.3.1 (from -r requirements-freeze.txt (line 84))
  Using cached transforms3d-0.3.1.tar.gz (62 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting types-setuptools==57.4.14 (from -r requirements-freeze.txt (line 85))
  Using cached types_setuptools-57.4.14-py3-none-any.whl.metadata (1.2 kB)
Collecting typing_extensions==4.2.0 (from -r requirements-freeze.txt (line 86))
  Using cached typing_extensions-4.2.0-py3-none-any.whl.metadata (6.2 kB)
Collecting urllib3==1.26.9 (from -r requirements-freeze.txt (line 87))
  Using cached urllib3-1.26.9-py2.py3-none-any.whl.metadata (46 kB)
Collecting Werkzeug==2.1.2 (from -r requirements-freeze.txt (line 88))
  Using cached Werkzeug-2.1.2-py3-none-any.whl.metadata (4.4 kB)
Collecting wquantiles==0.6 (from -r requirements-freeze.txt (line 89))
  Using cached wquantiles-0.6-py3-none-any.whl.metadata (1.1 kB)
Collecting wrapt==1.14.0 (from -r requirements-freeze.txt (line 90))
  Using cached wrapt-1.14.0-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (6.7 kB)
Collecting xlwt==1.3.0 (from -r requirements-freeze.txt (line 91))
  Using cached xlwt-1.3.0-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting zipp==3.8.0 (from -r requirements-freeze.txt (line 92))
  Using cached zipp-3.8.0-py3-none-any.whl.metadata (2.7 kB)
Collecting torch==1.5.0 (from -r requirements-freeze.txt (line 97))
  Using cached torch-1.5.0-cp37-none-macosx_10_9_x86_64.whl.metadata (1.4 kB)
Collecting torchvision==0.6.0 (from -r requirements-freeze.txt (line 99))
  Using cached torchvision-0.6.0-cp37-cp37m-macosx_10_9_x86_64.whl.metadata (4.1 kB)
Collecting torchio>=0.18.68 (from ivadomed==2.9.5->-r requirements-freeze.txt (line 30))
  Using cached torchio-0.18.92-py2.py3-none-any.whl.metadata (46 kB)
Collecting setuptools (from nibabel==3.2.2->-r requirements-freeze.txt (line 40))
  Using cached setuptools-68.0.0-py3-none-any.whl.metadata (6.4 kB)
Collecting wheel>=0.26 (from tensorboard==1.15.0->-r requirements-freeze.txt (line 76))
  Using cached wheel-0.42.0-py3-none-any.whl.metadata (2.2 kB)
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Successfully built docopt future gast SQLAlchemy termcolor transforms3d
Installing collected packages: xlwt, types-setuptools, transforms3d, termcolor, tensorflow-estimator, SimpleITK, raven, pytz, PyQt5_sip, iniconfig, docopt, dictdiffer, certifi, bids-validator, zipp, wrapt, wheel, Werkzeug, urllib3, typing_extensions, tqdm, tomli, threadpoolctl, SQLAlchemy, six, shellingham, setuptools, requirements-parser, PyYAML, PyQt5, pyparsing, pygments, pycparser, py, psutil, protobuf, portalocker, Pillow, numpy, num2words, networkx, mdurl, loguru, joblib, interface-meta, idna, gast, future, fonttools, cycler, coverage, charset-normalizer, attrs, astor, wquantiles, torch, tifffile, scipy, requests, PyWavelets, python-dateutil, packaging, opt-einsum, onnxruntime, markdown-it-py, kiwisolver, Keras-Preprocessing, importlib-metadata, imageio, h5py, grpcio, google-pasta, Deprecated, cffi, absl-py, torchvision, scikit-learn, scikit-image, rich, pluggy, pandas, nibabel, matplotlib, Markdown, Keras-Applications, humanize, cryptography, click, typer, tensorboard, seaborn, pytest, pyOpenSSL, Keras, formulaic, dipy, csv-diff, tensorflow, pytest-cov, pytest-console-scripts, pybids, torchio, ivadomed
Successfully installed Deprecated-1.2.13 Keras-2.3.1 Keras-Applications-1.0.8 Keras-Preprocessing-1.1.2 Markdown-3.3.6 Pillow-9.1.0 PyQt5-5.11.3 PyQt5_sip-4.19.19 PyWavelets-1.3.0 PyYAML-6.0 SQLAlchemy-1.3.24 SimpleITK-2.1.1.2 Werkzeug-2.1.2 absl-py-1.0.0 astor-0.7.1 attrs-21.4.0 bids-validator-1.9.3 certifi-2021.10.8 cffi-1.15.0 charset-normalizer-2.0.12 click-8.1.3 coverage-6.3.2 cryptography-37.0.1 csv-diff-1.1 cycler-0.11.0 dictdiffer-0.9.0 dipy-1.5.0 docopt-0.6.2 fonttools-4.33.3 formulaic-0.3.3 future-0.18.2 gast-0.2.2 google-pasta-0.2.0 grpcio-1.44.0 h5py-2.10.0 humanize-4.0.0 idna-3.3 imageio-2.18.0 importlib-metadata-4.11.3 iniconfig-1.1.1 interface-meta-1.3.0 ivadomed-2.9.5 joblib-1.1.0 kiwisolver-1.4.2 loguru-0.6.0 markdown-it-py-2.2.0 matplotlib-3.5.1 mdurl-0.1.2 networkx-2.6.3 nibabel-3.2.2 num2words-0.5.10 numpy-1.18.5 onnxruntime-1.7.0 opt-einsum-3.3.0 packaging-21.3 pandas-1.3.5 pluggy-1.0.0 portalocker-2.4.0 protobuf-3.20.1 psutil-5.9.0 py-1.11.0 pyOpenSSL-22.0.0 pybids-0.15.1 pycparser-2.21 pygments-2.17.2 pyparsing-2.4.7 pytest-7.1.2 pytest-console-scripts-1.3.1 pytest-cov-3.0.0 python-dateutil-2.8.2 pytz-2022.1 raven-6.10.0 requests-2.27.1 requirements-parser-0.5.0 rich-13.8.1 scikit-image-0.19.2 scikit-learn-1.0.2 scipy-1.7.3 seaborn-0.11.2 setuptools-65.6.3 shellingham-1.5.4 six-1.16.0 tensorboard-1.15.0 tensorflow-1.15.5 tensorflow-estimator-1.15.1 termcolor-1.1.0 threadpoolctl-3.1.0 tifffile-2021.11.2 tomli-2.0.1 torch-1.5.0 torchio-0.18.92 torchvision-0.6.0 tqdm-4.64.0 transforms3d-0.3.1 typer-0.12.5 types-setuptools-57.4.14 typing_extensions-4.2.0 urllib3-1.26.9 wheel-0.38.4 wquantiles-0.6 wrapt-1.14.0 xlwt-1.3.0 zipp-3.8.0

Installing spinalcordtoolbox...

Obtaining file:///Users/davidwarrenmartin/sct_5.6
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-5.6

AVX is supported on this macOS machine. Keeping default TensorFlow...


Creating launchers for Python scripts...


Installing binaries...


sct_download_data -d binaries_osx -k


--
Spinal Cord Toolbox (5.6)

sct_download_data -d binaries_osx -k
--

Trying URL: https://osf.io/874cy?action=download
Downloading: 20200801_sct_binaries_osx.tar.gz

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Status: 100%|██████████| 60.8M/60.8M [00:02<00:00, 22.2MB/s]Creating temporary folder (/var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150250.122138-o9_76c7k)
Unzip data to: /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150250.122138-o9_76c7k
Copying data to: /Users/davidwarrenmartin/sct_5.6/bin
Removing temporary folders...

Done!


All requirements installed!


Installing data...


rm -rf /Users/davidwarrenmartin/sct_5.6/data


mkdir -p /Users/davidwarrenmartin/sct_5.6/data


sct_download_data -d PAM50


--
Spinal Cord Toolbox (5.6)

sct_download_data -d PAM50
--

Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20201104/PAM50-r20201104.zip
Downloading: PAM50-r20201104.zip

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Status: 100%|██████████| 70.9M/70.9M [00:03<00:00, 19.3MB/s]Creating temporary folder (/var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150256.990578-_2vw3mu8)
Unzip data to: /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150256.990578-_2vw3mu8
Copying data to: /Users/davidwarrenmartin/sct_5.6/data/PAM50
Removing temporary folders...

Done!


sct_download_data -d gm_model


--
Spinal Cord Toolbox (5.6)

sct_download_data -d gm_model
--

Trying URL: https://osf.io/ugscu/?action=download
Downloading: 20160922_gm_model.zip

Status:   0%|          | 0.00/10.3M [00:00<?, ?B/s]
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Status: 100%|██████████| 10.3M/10.3M [00:00<00:00, 20.5MB/s]Creating temporary folder (/var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150259.549597-diaxnhs1)
Unzip data to: /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150259.549597-diaxnhs1
Copying data to: /Users/davidwarrenmartin/sct_5.6/data/gm_model
Removing temporary folders...

Done!


sct_download_data -d optic_models


--
Spinal Cord Toolbox (5.6)

sct_download_data -d optic_models
--

Trying URL: https://github.com/spinalcordtoolbox/optic_models/releases/download/r20170413/20170413_optic_models.zip
Downloading: 20170413_optic_models.zip

Status:   0%|          | 0.00/17.7k [00:00<?, ?B/s]
Status: 100%|██████████| 17.7k/17.7k [00:00<00:00, 28.2MB/s]Creating temporary folder (/var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150300.890060-h560lw70)
Unzip data to: /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150300.890060-h560lw70
Copying data to: /Users/davidwarrenmartin/sct_5.6/data/optic_models
Removing temporary folders...

Done!


sct_download_data -d pmj_models


--
Spinal Cord Toolbox (5.6)

sct_download_data -d pmj_models
--

Trying URL: https://github.com/spinalcordtoolbox/pmj_models/releases/download/r20170922/20170922_pmj_models.zip
Downloading: 20170922_pmj_models.zip

Status:   0%|          | 0.00/8.87k [00:00<?, ?B/s]
Status: 100%|██████████| 8.87k/8.87k [00:00<00:00, 13.4MB/s]Creating temporary folder (/var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150302.118551-asv4jidn)
Unzip data to: /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150302.118551-asv4jidn
Copying data to: /Users/davidwarrenmartin/sct_5.6/data/pmj_models
Removing temporary folders...

Done!


sct_download_data -d deepseg_sc_models


--
Spinal Cord Toolbox (5.6)

sct_download_data -d deepseg_sc_models
--

Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20180610_deepseg_sc_models.zip
Downloading: 20180610_deepseg_sc_models.zip

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Status: 100%|██████████| 58.7M/58.7M [00:02<00:00, 19.8MB/s]Creating temporary folder (/var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150306.314734-9bnt1u2p)
Unzip data to: /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150306.314734-9bnt1u2p
Copying data to: /Users/davidwarrenmartin/sct_5.6/data/deepseg_sc_models
Removing temporary folders...

Done!


sct_download_data -d deepseg_gm_models


--
Spinal Cord Toolbox (5.6)

sct_download_data -d deepseg_gm_models
--

Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20180205_deepseg_gm_models.zip
Downloading: 20180205_deepseg_gm_models.zip

Status:   0%|          | 0.00/2.28M [00:00<?, ?B/s]
Status:  35%|███▌      | 803k/2.28M [00:00<00:00, 8.00MB/s]
Status: 100%|██████████| 2.28M/2.28M [00:00<00:00, 11.4MB/s]Creating temporary folder (/var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150308.461792-ggiequya)
Unzip data to: /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150308.461792-ggiequya
Copying data to: /Users/davidwarrenmartin/sct_5.6/data/deepseg_gm_models
Removing temporary folders...

Done!


sct_download_data -d deepseg_lesion_models


--
Spinal Cord Toolbox (5.6)

sct_download_data -d deepseg_lesion_models
--

Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20180613_deepseg_lesion_models.zip
Downloading: 20180613_deepseg_lesion_models.zip

Status:   0%|          | 0.00/16.0M [00:00<?, ?B/s]
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Status: 100%|██████████| 16.0M/16.0M [00:00<00:00, 20.9MB/s]Creating temporary folder (/var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150310.494892-5fz_lm9n)
Unzip data to: /var/folders/db/2nwfsln942q61h6fp_bt5ymh0000gn/T/sct-20240916150310.494892-5fz_lm9n
Copying data to: /Users/davidwarrenmartin/sct_5.6/data/deepseg_lesion_models
Removing temporary folders...

Done!


sct_download_data -d c2c3_disc_models


--
Spinal Cord Toolbox (5.6)

sct_download_data -d c2c3_disc_models
--

Trying URL: https://github.com/spinalcordtoolbox/c2c3_disc_models/releases/download/r20190117/20190117_c2c3_disc_models.zip
Downloading: 20190117_c2c3_disc_models.zip

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Validate installation...


--
Spinal Cord Toolbox (5.6)

sct_check_dependencies 
--

SCT info:
- version: 5.6
- path: /Users/davidwarrenmartin/sct_5.6
OS: osx (Darwin-17.7.0-x86_64-i386-64bit)
CPU cores: Available: 4, Used by ITK functions: 4
RAM: Total: 8192MB, Used: 4960MB, Available: 2776MB
Check Python executable.............................[OK]
  Using bundled python 3.7.16 (default, Jan 17 2023, 09:28:58) 
[Clang 14.0.6 ] at /Users/davidwarrenmartin/sct_5.6/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Traceback (most recent call last):
  File "/Users/davidwarrenmartin/sct_5.6/spinalcordtoolbox/scripts/sct_check_dependencies.py", line 386, in <module>
    main(sys.argv[1:])
  File "/Users/davidwarrenmartin/sct_5.6/spinalcordtoolbox/scripts/sct_check_dependencies.py", line 261, in main
    import matplotlib.pyplot as plt
  File "/Users/davidwarrenmartin/sct_5.6/python/envs/venv_sct/lib/python3.7/site-packages/matplotlib/__init__.py", line 109, in <module>
    from . import _api, _version, cbook, docstring, rcsetup
  File "/Users/davidwarrenmartin/sct_5.6/python/envs/venv_sct/lib/python3.7/site-packages/matplotlib/rcsetup.py", line 27, in <module>
    from matplotlib.colors import Colormap, is_color_like
  File "/Users/davidwarrenmartin/sct_5.6/python/envs/venv_sct/lib/python3.7/site-packages/matplotlib/colors.py", line 51, in <module>
    from PIL import Image
  File "/Users/davidwarrenmartin/sct_5.6/python/envs/venv_sct/lib/python3.7/site-packages/PIL/Image.py", line 132, in <module>
    from . import _imaging as core
ImportError: dlopen(/Users/davidwarrenmartin/sct_5.6/python/envs/venv_sct/lib/python3.7/site-packages/PIL/_imaging.cpython-37m-darwin.so, 2): Symbol not found: ____chkstk_darwin
  Referenced from: /Users/davidwarrenmartin/sct_5.6/python/envs/venv_sct/lib/python3.7/site-packages/PIL/.dylibs/libtiff.5.dylib (which was built for Mac OS X 11.0)
  Expected in: /usr/lib/libSystem.B.dylib
 in /Users/davidwarrenmartin/sct_5.6/python/envs/venv_sct/lib/python3.7/site-packages/PIL/.dylibs/libtiff.5.dylib

Installation validation Failed!


Installation failed!

Please find the file "/Users/davidwarrenmartin/Desktop/Research/CSF_Flow/Spinal_Cord_Toolbox/spinalcordtoolbox-5.6/install_sct_log.txt",
then upload it as a .txt attachment in a new topic on SCT's forum:
--> http://forum.spinalcordmri.org/c/sct