audreyb@DESKTOP-SFQA0JM:~/sct$ ./install_sct -y
 non-interactive mode


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



Checking OS type and version...

Linux DESKTOP-SFQA0JM 5.4.72-microsoft-standard-WSL2 #1 SMP Wed Oct 28 23:40:43 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements...


OK!


SCT version ......... dev
Installation type ... in-place
Operating system .... linux (unknown)
Shell config ........ /home/audreyb/.bashrc

--> Crash reports will not be sent.


SCT will be installed here: [/home/audreyb/sct]


Skipping copy of source files (source and destination folders are the same)


Installing conda...


rm -rf /home/audreyb/sct/python


mkdir -p /home/audreyb/sct/python


wget -nv -O /tmp/tmp.QhY8G6xiE6/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

2021-08-09 10:13:10 URL:https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [66709754/66709754] -> "/tmp/tmp.QhY8G6xiE6/miniconda.sh" [1]

bash /tmp/tmp.QhY8G6xiE6/miniconda.sh -p /home/audreyb/sct/python -b -f

PREFIX=/home/audreyb/sct/python
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/audreyb/sct/python

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - _openmp_mutex==4.5=1_gnu
    - brotlipy==0.7.0=py39h27cfd23_1003
    - ca-certificates==2021.7.5=h06a4308_1
    - certifi==2021.5.30=py39h06a4308_0
    - cffi==1.14.6=py39h400218f_0
    - chardet==4.0.0=py39h06a4308_1003
    - conda-package-handling==1.7.3=py39h27cfd23_1
    - conda==4.10.3=py39h06a4308_0
    - cryptography==3.4.7=py39hd23ed53_0
    - idna==2.10=pyhd3eb1b0_0
    - ld_impl_linux-64==2.35.1=h7274673_9
    - libffi==3.3=he6710b0_2
    - libgcc-ng==9.3.0=h5101ec6_17
    - libgomp==9.3.0=h5101ec6_17
    - libstdcxx-ng==9.3.0=hd4cf53a_17
    - ncurses==6.2=he6710b0_1
    - openssl==1.1.1k=h27cfd23_0
    - pip==21.1.3=py39h06a4308_0
    - pycosat==0.6.3=py39h27cfd23_0
    - pycparser==2.20=py_2
    - pyopenssl==20.0.1=pyhd3eb1b0_1
    - pysocks==1.7.1=py39h06a4308_0
    - python==3.9.5=h12debd9_4
    - readline==8.1=h27cfd23_0
    - requests==2.25.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py39h27cfd23_0
    - setuptools==52.0.0=py39h06a4308_0
    - six==1.16.0=pyhd3eb1b0_0
    - sqlite==3.36.0=hc218d9a_0
    - tk==8.6.10=hbc83047_0
    - tqdm==4.61.2=pyhd3eb1b0_1
    - tzdata==2021a=h52ac0ba_0
    - urllib3==1.26.6=pyhd3eb1b0_1
    - wheel==0.36.2=pyhd3eb1b0_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.2.5=h7b6447c_0
    - zlib==1.2.11=h7b6447c_3


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  brotlipy           pkgs/main/linux-64::brotlipy-0.7.0-py39h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.7.5-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.5.30-py39h06a4308_0
  cffi               pkgs/main/linux-64::cffi-1.14.6-py39h400218f_0
  chardet            pkgs/main/linux-64::chardet-4.0.0-py39h06a4308_1003
  conda              pkgs/main/linux-64::conda-4.10.3-py39h06a4308_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.3-py39h27cfd23_1
  cryptography       pkgs/main/linux-64::cryptography-3.4.7-py39hd23ed53_0
  idna               pkgs/main/noarch::idna-2.10-pyhd3eb1b0_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1k-h27cfd23_0
  pip                pkgs/main/linux-64::pip-21.1.3-py39h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py39h27cfd23_0
  pycparser          pkgs/main/noarch::pycparser-2.20-py_2
  pyopenssl          pkgs/main/noarch::pyopenssl-20.0.1-pyhd3eb1b0_1
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py39h06a4308_0
  python             pkgs/main/linux-64::python-3.9.5-h12debd9_4
  readline           pkgs/main/linux-64::readline-8.1-h27cfd23_0
  requests           pkgs/main/noarch::requests-2.25.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.100-py39h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-52.0.0-py39h06a4308_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_0
  sqlite             pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.10-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.61.2-pyhd3eb1b0_1
  tzdata             pkgs/main/noarch::tzdata-2021a-h52ac0ba_0
  urllib3            pkgs/main/noarch::urllib3-1.26.6-pyhd3eb1b0_1
  wheel              pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Preparing transaction: done
Executing transaction: done
installation finished.
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/audreyb/sct/python/envs/venv_sct

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2021.5.30          |   py36h06a4308_0         139 KB
    pip-21.2.2                 |   py36h06a4308_0         1.8 MB
    python-3.6.13              |       h12debd9_1        32.5 MB
    setuptools-52.0.0          |   py36h06a4308_0         724 KB
    ------------------------------------------------------------
                                           Total:        35.2 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.7.5-h06a4308_1
  certifi            pkgs/main/linux-64::certifi-2021.5.30-py36h06a4308_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1k-h27cfd23_0
  pip                pkgs/main/linux-64::pip-21.2.2-py36h06a4308_0
  python             pkgs/main/linux-64::python-3.6.13-h12debd9_1
  readline           pkgs/main/linux-64::readline-8.1-h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-52.0.0-py36h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.10-hbc83047_0
  wheel              pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3



Downloading and Extracting Packages
setuptools-52.0.0    | 724 KB    | ############################################################################# | 100%
python-3.6.13        | 32.5 MB   | ############################################################################# | 100%
pip-21.2.2           | 1.8 MB    | ############################################################################# | 100%
certifi-2021.5.30    | 139 KB    | ############################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate


Installing Python dependencies...


Using requirements.txt (git installation)

Looking in links: https://download.pytorch.org/whl/cpu/torch_stable.html
Ignoring torch: markers 'sys_platform == "darwin"' don't match your environment
Ignoring torchvision: markers 'sys_platform == "darwin"' don't match your environment
Collecting colored
  Using cached colored-1.4.2.tar.gz (56 kB)
Collecting dipy
  Using cached dipy-1.4.1-cp36-cp36m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (7.7 MB)
Collecting futures
  Using cached futures-3.1.1-py3-none-any.whl (2.8 kB)
Collecting h5py~=2.10.0
  Downloading h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB)
     |████████████████████████████████| 2.9 MB 2.3 MB/s
Collecting Keras==2.1.5
  Downloading Keras-2.1.5-py2.py3-none-any.whl (334 kB)
     |████████████████████████████████| 334 kB 5.6 MB/s
Collecting ivadomed
  Downloading ivadomed-2.7.4-py3-none-any.whl (155 kB)
     |████████████████████████████████| 155 kB 5.2 MB/s
Collecting matplotlib
  Downloading matplotlib-3.3.4-cp36-cp36m-manylinux1_x86_64.whl (11.5 MB)
     |████████████████████████████████| 11.5 MB 290 kB/s
Collecting nibabel
  Downloading nibabel-3.2.1-py3-none-any.whl (3.3 MB)
     |████████████████████████████████| 3.3 MB 33 kB/s
Collecting numpy
  Downloading numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl (14.8 MB)
     |████████████████████████████████| 14.8 MB 34 kB/s
Collecting onnxruntime==1.4.0
  Downloading onnxruntime-1.4.0-cp36-cp36m-manylinux2010_x86_64.whl (4.4 MB)
     |████████████████████████████████| 4.4 MB 6.0 MB/s
Collecting pandas
  Downloading pandas-1.1.5-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB)
     |████████████████████████████████| 9.5 MB 7.0 MB/s
Collecting psutil
  Downloading psutil-5.8.0-cp36-cp36m-manylinux2010_x86_64.whl (291 kB)
     |████████████████████████████████| 291 kB 6.9 MB/s
Collecting pyqt5==5.11.3
  Downloading PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8 MB)
     |████████████████████████████████| 117.8 MB 6.1 MB/s
Collecting pytest
  Downloading pytest-6.2.4-py3-none-any.whl (280 kB)
     |████████████████████████████████| 280 kB 5.3 MB/s
Collecting pytest-cov
  Downloading pytest_cov-2.12.1-py2.py3-none-any.whl (20 kB)
Collecting raven
  Downloading raven-6.10.0-py2.py3-none-any.whl (284 kB)
     |████████████████████████████████| 284 kB 5.7 MB/s
Collecting requests
  Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB)
     |████████████████████████████████| 62 kB 11 kB/s
Collecting requirements-parser
  Downloading requirements-parser-0.2.0.tar.gz (6.3 kB)
Collecting scipy
  Downloading scipy-1.5.4-cp36-cp36m-manylinux1_x86_64.whl (25.9 MB)
     |████████████████████████████████| 25.9 MB 7.9 MB/s
Collecting scikit-image
  Downloading scikit_image-0.17.2-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB)
     |████████████████████████████████| 12.4 MB 5.1 MB/s
Collecting scikit-learn
  Downloading scikit_learn-0.24.2-cp36-cp36m-manylinux2010_x86_64.whl (22.2 MB)
     |████████████████████████████████| 22.2 MB 22 kB/s
Collecting tensorflow==1.5.0
  Downloading tensorflow-1.5.0-cp36-cp36m-manylinux1_x86_64.whl (44.4 MB)
     |████████████████████████████████| 44.4 MB 5.4 MB/s
Collecting torch==1.5.0+cpu
  Downloading https://download.pytorch.org/whl/cpu/torch-1.5.0%2Bcpu-cp36-cp36m-linux_x86_64.whl (127.3 MB)
     |████████████████████████████████| 127.3 MB 106 kB/s
Collecting torchvision==0.6.0+cpu
  Downloading https://download.pytorch.org/whl/cpu/torchvision-0.6.0%2Bcpu-cp36-cp36m-linux_x86_64.whl (5.7 MB)
     |████████████████████████████████| 5.7 MB 101 kB/s
Collecting xlwt
  Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
     |████████████████████████████████| 99 kB 106 kB/s
Collecting tqdm
  Downloading tqdm-4.62.0-py2.py3-none-any.whl (76 kB)
     |████████████████████████████████| 76 kB 1.9 MB/s
Collecting transforms3d
  Downloading transforms3d-0.3.1.tar.gz (62 kB)
     |████████████████████████████████| 62 kB 695 kB/s
Collecting urllib3[secure]
  Downloading urllib3-1.26.6-py2.py3-none-any.whl (138 kB)
     |████████████████████████████████| 138 kB 2.4 MB/s
Collecting pytest_console_scripts
  Downloading pytest-console-scripts-1.2.0.tar.gz (13 kB)
Collecting wquantiles
  Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)
Collecting six>=1.9.0
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pyyaml
  Downloading PyYAML-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (640 kB)
     |████████████████████████████████| 640 kB 5.1 MB/s
Collecting protobuf
  Downloading protobuf-3.17.3-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.0 MB)
     |████████████████████████████████| 1.0 MB 4.9 MB/s
Collecting PyQt5_sip<4.20,>=4.19.11
  Downloading PyQt5_sip-4.19.19-cp36-cp36m-manylinux1_x86_64.whl (67 kB)
     |████████████████████████████████| 67 kB 2.2 MB/s
Collecting absl-py>=0.1.6
  Downloading absl_py-0.13.0-py3-none-any.whl (132 kB)
     |████████████████████████████████| 132 kB 5.4 MB/s
Collecting tensorflow-tensorboard<1.6.0,>=1.5.0
  Downloading tensorflow_tensorboard-1.5.1-py3-none-any.whl (3.0 MB)
     |████████████████████████████████| 3.0 MB 5.4 MB/s
Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorflow==1.5.0->-r requirements.txt (line 27)) (0.36.2)
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
     |████████████████████████████████| 829 kB 5.5 MB/s
Collecting pillow>=4.1.1
  Downloading Pillow-8.3.1-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (3.0 MB)
     |████████████████████████████████| 3.0 MB 6.3 MB/s
Collecting joblib
  Downloading joblib-1.0.1-py3-none-any.whl (303 kB)
     |████████████████████████████████| 303 kB 5.5 MB/s
Collecting pytest-ordering
  Downloading pytest_ordering-0.6-py3-none-any.whl (4.6 kB)
Collecting tensorboard
  Downloading tensorboard-2.6.0-py3-none-any.whl (5.6 MB)
     |████████████████████████████████| 5.6 MB 5.0 MB/s
Collecting csv-diff>=1.0
  Downloading csv_diff-1.1-py3-none-any.whl (12 kB)
Collecting pre-commit==2.10.1
  Downloading pre_commit-2.10.1-py2.py3-none-any.whl (185 kB)
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Collecting sphinx-jsonschema
  Downloading sphinx-jsonschema-1.16.11.tar.gz (15 kB)
Collecting bids-neuropoly>=0.2
  Downloading bids_neuropoly-0.2-py3-none-any.whl (3.1 kB)
Collecting pybids>=0.12.4
  Downloading pybids-0.13.1-py3-none-any.whl (3.2 MB)
     |████████████████████████████████| 3.2 MB 5.3 MB/s
Collecting seaborn
  Downloading seaborn-0.11.1-py3-none-any.whl (285 kB)
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Collecting identify>=1.0.0
  Downloading identify-2.2.13-py2.py3-none-any.whl (98 kB)
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Collecting cfgv>=2.0.0
  Downloading cfgv-3.3.0-py2.py3-none-any.whl (7.3 kB)
Collecting nodeenv>=0.11.1
  Downloading nodeenv-1.6.0-py2.py3-none-any.whl (21 kB)
Collecting toml
  Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)
Collecting importlib-resources
  Downloading importlib_resources-5.2.2-py3-none-any.whl (27 kB)
Collecting importlib-metadata
  Downloading importlib_metadata-4.6.3-py3-none-any.whl (17 kB)
Collecting virtualenv>=20.0.8
  Downloading virtualenv-20.7.0-py2.py3-none-any.whl (5.3 MB)
     |████████████████████████████████| 5.3 MB 6.4 MB/s
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB)
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Collecting cycler>=0.10
  Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
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Collecting python-dateutil>=2.1
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
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Collecting packaging>=14.3
  Downloading packaging-21.0-py3-none-any.whl (40 kB)
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Collecting pytz>=2017.2
  Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB)
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Collecting attrs>=19.2.0
  Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB)
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Collecting iniconfig
  Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB)
Collecting pluggy<1.0.0a1,>=0.12
  Downloading pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting py>=1.8.2
  Downloading py-1.10.0-py2.py3-none-any.whl (97 kB)
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Collecting coverage>=5.2.1
  Downloading coverage-5.5-cp36-cp36m-manylinux2010_x86_64.whl (240 kB)
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Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests->-r requirements.txt (line 22)) (2021.5.30)
Collecting charset-normalizer~=2.0.0
  Downloading charset_normalizer-2.0.4-py3-none-any.whl (36 kB)
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Collecting typing-extensions>=3.6.4
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Collecting decorator<5,>=4.3
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Collecting num2words
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Collecting bids-validator
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Collecting html5lib==0.9999999
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Collecting bleach==1.5.0
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Collecting backports.entry-points-selectable>=1.0.4
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Collecting filelock<4,>=3.0.0
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Collecting jsonpointer
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Collecting grpcio>=1.24.3
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Requirement already satisfied: setuptools>=41.0.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard->ivadomed->-r requirements.txt (line 8)) (52.0.0.post20210125)
Collecting tensorboard-plugin-wit>=1.6.0
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Collecting rsa<5,>=3.1.4
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Collecting cachetools<5.0,>=2.0.0
  Downloading cachetools-4.2.2-py3-none-any.whl (11 kB)
Collecting requests-oauthlib>=0.7.0
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Building wheels for collected packages: colored, requirements-parser, transforms3d, pytest-console-scripts, html5lib, future, docopt, sphinx-jsonschema
  Building wheel for colored (setup.py) ... done
  Created wheel for colored: filename=colored-1.4.2-py3-none-any.whl size=14003 sha256=f2393399cbd97bc036a84bcd45575fb865e7231ef5dd613da4cb34567bda6214
  Stored in directory: /home/audreyb/.cache/pip/wheels/b7/be/ae/a98f7701429c3cfcebf4d2b537e48a1571549a4d8b55463a01
  Building wheel for requirements-parser (setup.py) ... done
  Created wheel for requirements-parser: filename=requirements_parser-0.2.0-py3-none-any.whl size=7655 sha256=1640eb516370a51b3d464911156503548532c042c4b26f710517e5616a35149f
  Stored in directory: /home/audreyb/.cache/pip/wheels/80/af/bd/32c202b632c3e9a1b482b33d37f5efd128137891a08f3c3bae
  Building wheel for transforms3d (setup.py) ... done
  Created wheel for transforms3d: filename=transforms3d-0.3.1-py3-none-any.whl size=59374 sha256=364e875f84f9911f03f20b7f6f532ba9bd7a25af4c637928274aa8424f6a8cd8
  Stored in directory: /home/audreyb/.cache/pip/wheels/be/7a/eb/465e9bb085af816c4d504821d542cc0059cc3433f6e8edea3c
  Building wheel for pytest-console-scripts (setup.py) ... done
  Created wheel for pytest-console-scripts: filename=pytest_console_scripts-1.2.0-py3-none-any.whl size=9106 sha256=1cb8ae29e997273d3c7e4e1f78bced20378dc1b7dde6faa46fb1c5bf1dd5116a
  Stored in directory: /home/audreyb/.cache/pip/wheels/b4/5e/10/1169e05aa99eb21b2d66be1fd0f80c7305f1ec9492cac35eb9
  Building wheel for html5lib (setup.py) ... done
  Created wheel for html5lib: filename=html5lib-0.9999999-py3-none-any.whl size=107219 sha256=8298f0603b5b7ec39ee9b9ffd0177760a962ab174b9302b5f82f6ec9a6370a14
  Stored in directory: /home/audreyb/.cache/pip/wheels/90/1c/cb/a87fd097ff74648ecc468a703001f6c7c86d8a71d459e65c98
  Building wheel for future (setup.py) ... done
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=25f5622122b0342a2445ac8f8fc6f720d55b1a2f764896c2262a49607a208a31
  Stored in directory: /home/audreyb/.cache/pip/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94
  Building wheel for docopt (setup.py) ... done
  Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=4c8c752a7b17a704efd6c79a38a2952570f913d0441818d51385250a791e2027
  Stored in directory: /home/audreyb/.cache/pip/wheels/3f/2a/fa/4d7a888e69774d5e6e855d190a8a51b357d77cc05eb1c097c9
  Building wheel for sphinx-jsonschema (setup.py) ... done
  Created wheel for sphinx-jsonschema: filename=sphinx_jsonschema-1.16.11-py3-none-any.whl size=12803 sha256=e33548cd2ee58f927d3718a62b368b93f678fd0e54498ff2e002cdc6ba4384ee
  Stored in directory: /home/audreyb/.cache/pip/wheels/d2/95/d1/eaca961334123c35c99970c340e78c1fc9824395aa99eca8b3
Successfully built colored requirements-parser transforms3d pytest-console-scripts html5lib future docopt sphinx-jsonschema
Installing collected packages: zipp, urllib3, typing-extensions, six, pyparsing, pyasn1, idna, charset-normalizer, rsa, requests, pytz, python-dateutil, pycparser, pyasn1-modules, packaging, oauthlib, numpy, importlib-metadata, docopt, cachetools, toml, sqlalchemy, scipy, requests-oauthlib, py, pluggy, platformdirs, pillow, patsy, pandas, num2words, nibabel, kiwisolver, iniconfig, importlib-resources, html5lib, google-auth, future, filelock, distlib, decorator, dataclasses, cycler, click, cffi, bids-validator, backports.entry-points-selectable, attrs, werkzeug, virtualenv, torch, tifffile, threadpoolctl, tensorboard-plugin-wit, tensorboard-data-server, pyyaml, PyWavelets, pytest, pybids, protobuf, nodeenv, networkx, mock, matplotlib, markdown, jsonpointer, joblib, imageio, identify, grpcio, google-auth-oauthlib, docutils, dictdiffer, cryptography, cfgv, bleach, absl-py, tqdm, torchvision, tensorflow-tensorboard, tensorboard, sphinx-jsonschema, seaborn, scikit-learn, scikit-image, pytest-ordering, pytest-console-scripts, PyQt5-sip, pyOpenSSL, pre-commit, onnxruntime, h5py, csv-diff, coverage, bids-neuropoly, xlwt, wquantiles, transforms3d, tensorflow, requirements-parser, raven, pytest-cov, pyqt5, psutil, Keras, ivadomed, futures, dipy, colored
Successfully installed Keras-2.1.5 PyQt5-sip-4.19.19 PyWavelets-1.1.1 absl-py-0.13.0 attrs-21.2.0 backports.entry-points-selectable-1.1.0 bids-neuropoly-0.2 bids-validator-1.8.0 bleach-1.5.0 cachetools-4.2.2 cffi-1.14.6 cfgv-3.3.0 charset-normalizer-2.0.4 click-8.0.1 colored-1.4.2 coverage-5.5 cryptography-3.4.7 csv-diff-1.1 cycler-0.10.0 dataclasses-0.8 decorator-4.4.2 dictdiffer-0.9.0 dipy-1.4.1 distlib-0.3.2 docopt-0.6.2 docutils-0.17.1 filelock-3.0.12 future-0.18.2 futures-3.1.1 google-auth-1.34.0 google-auth-oauthlib-0.4.5 grpcio-1.39.0 h5py-2.10.0 html5lib-0.9999999 identify-2.2.13 idna-3.2 imageio-2.9.0 importlib-metadata-4.6.3 importlib-resources-5.2.2 iniconfig-1.1.1 ivadomed-2.7.4 joblib-1.0.1 jsonpointer-2.1 kiwisolver-1.3.1 markdown-3.3.4 matplotlib-3.3.4 mock-4.0.3 networkx-2.5.1 nibabel-3.2.1 nodeenv-1.6.0 num2words-0.5.10 numpy-1.19.5 oauthlib-3.1.1 onnxruntime-1.4.0 packaging-21.0 pandas-1.1.5 patsy-0.5.1 pillow-8.3.1 platformdirs-2.2.0 pluggy-0.13.1 pre-commit-2.10.1 protobuf-3.17.3 psutil-5.8.0 py-1.10.0 pyOpenSSL-20.0.1 pyasn1-0.4.8 pyasn1-modules-0.2.8 pybids-0.13.1 pycparser-2.20 pyparsing-2.4.7 pyqt5-5.11.3 pytest-6.2.4 pytest-console-scripts-1.2.0 pytest-cov-2.12.1 pytest-ordering-0.6 python-dateutil-2.8.2 pytz-2021.1 pyyaml-5.4.1 raven-6.10.0 requests-2.26.0 requests-oauthlib-1.3.0 requirements-parser-0.2.0 rsa-4.7.2 scikit-image-0.17.2 scikit-learn-0.24.2 scipy-1.5.4 seaborn-0.11.1 six-1.16.0 sphinx-jsonschema-1.16.11 sqlalchemy-1.3.24 tensorboard-2.6.0 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.0 tensorflow-1.5.0 tensorflow-tensorboard-1.5.1 threadpoolctl-2.2.0 tifffile-2020.9.3 toml-0.10.2 torch-1.5.0+cpu torchvision-0.6.0+cpu tqdm-4.62.0 transforms3d-0.3.1 typing-extensions-3.10.0.0 urllib3-1.26.6 virtualenv-20.7.0 werkzeug-2.0.1 wquantiles-0.6 xlwt-1.3.0 zipp-3.5.0
Found existing installation: tensorflow-tensorboard 1.5.1
Uninstalling tensorflow-tensorboard-1.5.1:
  Successfully uninstalled tensorflow-tensorboard-1.5.1
Found existing installation: tensorboard 2.6.0
Uninstalling tensorboard-2.6.0:
  Successfully uninstalled tensorboard-2.6.0
Collecting tensorboard
  Using cached tensorboard-2.6.0-py3-none-any.whl (5.6 MB)
Requirement already satisfied: grpcio>=1.24.3 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (1.39.0)
Requirement already satisfied: protobuf>=3.6.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (3.17.3)
Requirement already satisfied: numpy>=1.12.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (1.19.5)
Requirement already satisfied: google-auth-oauthlib<0.5,>=0.4.1 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (0.4.5)
Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (1.8.0)
Requirement already satisfied: tensorboard-data-server<0.7.0,>=0.6.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (0.6.1)
Requirement already satisfied: absl-py>=0.4 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (0.13.0)
Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (0.36.2)
Requirement already satisfied: werkzeug>=0.11.15 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (2.0.1)
Requirement already satisfied: setuptools>=41.0.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (52.0.0.post20210125)
Requirement already satisfied: google-auth<2,>=1.6.3 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (1.34.0)
Requirement already satisfied: markdown>=2.6.8 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (3.3.4)
Requirement already satisfied: requests<3,>=2.21.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (2.26.0)
Requirement already satisfied: six in ./python/envs/venv_sct/lib/python3.6/site-packages (from absl-py>=0.4->tensorboard) (1.16.0)
Requirement already satisfied: pyasn1-modules>=0.2.1 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth<2,>=1.6.3->tensorboard) (0.2.8)
Requirement already satisfied: cachetools<5.0,>=2.0.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth<2,>=1.6.3->tensorboard) (4.2.2)
Requirement already satisfied: rsa<5,>=3.1.4 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth<2,>=1.6.3->tensorboard) (4.7.2)
Requirement already satisfied: requests-oauthlib>=0.7.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth-oauthlib<0.5,>=0.4.1->tensorboard) (1.3.0)
Requirement already satisfied: importlib-metadata in ./python/envs/venv_sct/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard) (4.6.3)
Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in ./python/envs/venv_sct/lib/python3.6/site-packages (from pyasn1-modules>=0.2.1->google-auth<2,>=1.6.3->tensorboard) (0.4.8)
Requirement already satisfied: charset-normalizer~=2.0.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard) (2.0.4)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard) (1.26.6)
Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard) (2021.5.30)
Requirement already satisfied: idna<4,>=2.5 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard) (3.2)
Requirement already satisfied: oauthlib>=3.0.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard) (3.1.1)
Requirement already satisfied: dataclasses in ./python/envs/venv_sct/lib/python3.6/site-packages (from werkzeug>=0.11.15->tensorboard) (0.8)
Requirement already satisfied: typing-extensions>=3.6.4 in ./python/envs/venv_sct/lib/python3.6/site-packages (from importlib-metadata->markdown>=2.6.8->tensorboard) (3.10.0.0)
Requirement already satisfied: zipp>=0.5 in ./python/envs/venv_sct/lib/python3.6/site-packages (from importlib-metadata->markdown>=2.6.8->tensorboard) (3.5.0)
Installing collected packages: tensorboard
Successfully installed tensorboard-2.6.0

Installing spinalcordtoolbox...

Obtaining file:///home/audreyb/sct
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-dev

Creating launchers for Python scripts...


Installing binaries...


sct_download_data -d binaries_linux -o /home/audreyb/sct/bin -k


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_download_data -d binaries_linux -o /home/audreyb/sct/bin -k
--

Trying URL: https://osf.io/cs6zt/?action=download
Downloading: 20200801_sct_binaries_linux.tar.gz
Status: 100%|██████████████████████████████████████████████████████████████████████| 78.2M/78.2M [00:23<00:00, 3.36MB/s]
Creating temporary folder (/tmp/sct-20210809102342.974620-kvkhhxyy)
Unzip data to: /tmp/sct-20210809102342.974620-kvkhhxyy
Removing temporary folders...
Done!


All requirements installed!


Installing data...


rm -rf /home/audreyb/sct/data


mkdir -p /home/audreyb/sct/data


sct_download_data -d PAM50 -o /home/audreyb/sct/data/PAM50


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_download_data -d PAM50 -o /home/audreyb/sct/data/PAM50
--

Removing existing destination folder '/home/audreyb/sct/data/PAM50'
Trying URL: https://github.com/sct-data/PAM50/releases/download/r20201104/PAM50-r20201104.zip
Downloading: PAM50-r20201104.zip
Status: 100%|██████████████████████████████████████████████████████████████████████| 70.9M/70.9M [00:24<00:00, 2.86MB/s]
Creating temporary folder (/tmp/sct-20210809102413.895016-61_d2or_)
Unzip data to: /tmp/sct-20210809102413.895016-61_d2or_
Removing temporary folders...
Done!


sct_download_data -d gm_model -o /home/audreyb/sct/data/gm_model


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_download_data -d gm_model -o /home/audreyb/sct/data/gm_model
--

Removing existing destination folder '/home/audreyb/sct/data/gm_model'
Trying URL: https://osf.io/ugscu/?action=download
Downloading: 20160922_gm_model.zip
Status: 100%|██████████████████████████████████████████████████████████████████████| 10.3M/10.3M [00:04<00:00, 2.17MB/s]
Creating temporary folder (/tmp/sct-20210809102429.682681-_hwy6spk)
Unzip data to: /tmp/sct-20210809102429.682681-_hwy6spk
Removing temporary folders...
Done!


sct_download_data -d optic_models -o /home/audreyb/sct/data/optic_models


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_download_data -d optic_models -o /home/audreyb/sct/data/optic_models
--

Removing existing destination folder '/home/audreyb/sct/data/optic_models'
Trying URL: https://github.com/sct-data/optic_models/releases/download/r20170413/20170413_optic_models.zip
Downloading: 20170413_optic_models.zip
Status: 100%|██████████████████████████████████████████████████████████████████████| 17.7k/17.7k [00:00<00:00, 53.3MB/s]
Creating temporary folder (/tmp/sct-20210809102430.737998-w8cniwno)
Unzip data to: /tmp/sct-20210809102430.737998-w8cniwno
Removing temporary folders...
Done!


sct_download_data -d pmj_models -o /home/audreyb/sct/data/pmj_models


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_download_data -d pmj_models -o /home/audreyb/sct/data/pmj_models
--

Removing existing destination folder '/home/audreyb/sct/data/pmj_models'
Trying URL: https://github.com/sct-data/pmj_models/releases/download/r20170922/20170922_pmj_models.zip
Downloading: 20170922_pmj_models.zip
Status: 100%|██████████████████████████████████████████████████████████████████████| 8.87k/8.87k [00:00<00:00, 27.9MB/s]
Creating temporary folder (/tmp/sct-20210809102431.593125-_hrmjyhz)
Unzip data to: /tmp/sct-20210809102431.593125-_hrmjyhz
Removing temporary folders...
Done!


sct_download_data -d deepseg_sc_models -o /home/audreyb/sct/data/deepseg_sc_models


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_download_data -d deepseg_sc_models -o /home/audreyb/sct/data/deepseg_sc_models
--

Removing existing destination folder '/home/audreyb/sct/data/deepseg_sc_models'
Trying URL: https://github.com/sct-data/deepseg_sc_models/releases/download/r20180610/20180610_deepseg_sc_models.zip
Downloading: 20180610_deepseg_sc_models.zip
Status: 100%|██████████████████████████████████████████████████████████████████████| 58.7M/58.7M [00:28<00:00, 2.05MB/s]
Creating temporary folder (/tmp/sct-20210809102501.110756-7i3gf3_k)
Unzip data to: /tmp/sct-20210809102501.110756-7i3gf3_k
Removing temporary folders...
Done!


sct_download_data -d deepseg_gm_models -o /home/audreyb/sct/data/deepseg_gm_models


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_download_data -d deepseg_gm_models -o /home/audreyb/sct/data/deepseg_gm_models
--

Removing existing destination folder '/home/audreyb/sct/data/deepseg_gm_models'
Trying URL: https://github.com/sct-data/deepseg_gm_models/releases/download/r20180205/20180205_deepseg_gm_models.zip
Downloading: 20180205_deepseg_gm_models.zip
Status: 100%|██████████████████████████████████████████████████████████████████████| 2.28M/2.28M [00:00<00:00, 4.46MB/s]
Creating temporary folder (/tmp/sct-20210809102503.144855-u9zpb9h6)
Unzip data to: /tmp/sct-20210809102503.144855-u9zpb9h6
Removing temporary folders...
Done!


sct_download_data -d deepseg_lesion_models -o /home/audreyb/sct/data/deepseg_lesion_models


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_download_data -d deepseg_lesion_models -o /home/audreyb/sct/data/deepseg_lesion_models
--

Removing existing destination folder '/home/audreyb/sct/data/deepseg_lesion_models'
Trying URL: https://github.com/sct-data/deepseg_lesion_models/releases/download/r20180613/20180613_deepseg_lesion_models.zip
Downloading: 20180613_deepseg_lesion_models.zip
Status: 100%|██████████████████████████████████████████████████████████████████████| 16.0M/16.0M [00:06<00:00, 2.60MB/s]
Creating temporary folder (/tmp/sct-20210809102510.445502-4he6akv7)
Unzip data to: /tmp/sct-20210809102510.445502-4he6akv7
Removing temporary folders...
Done!


sct_download_data -d c2c3_disc_models -o /home/audreyb/sct/data/c2c3_disc_models


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_download_data -d c2c3_disc_models -o /home/audreyb/sct/data/c2c3_disc_models
--

Removing existing destination folder '/home/audreyb/sct/data/c2c3_disc_models'
Trying URL: https://github.com/sct-data/c2c3_disc_models/releases/download/r20190117/20190117_c2c3_disc_models.zip
Downloading: 20190117_c2c3_disc_models.zip
Status: 100%|██████████████████████████████████████████████████████████████████████| 8.94k/8.94k [00:00<00:00, 32.9MB/s]
Creating temporary folder (/tmp/sct-20210809102511.717114-s693yl_i)
Unzip data to: /tmp/sct-20210809102511.717114-s693yl_i
Removing temporary folders...
Done!

Status: 100%|██████████████████████████████████████████████████████████████████████| 18.0M/18.0M [00:06<00:00, 2.83MB/s]

Validate installation...


--
Spinal Cord Toolbox (git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7)

sct_check_dependencies
--

SCT info:
- version: git-master-65c0b8be3b1be19fbb901be817a198f08a23c8c7
- path: /home/audreyb/sct
OS: linux (Linux-5.4.72-microsoft-standard-WSL2-x86_64-with-debian-buster-sid)
CPU cores: Available: 8, Used by ITK functions: 8
RAM: Total: 6172MB, Used: 111MB, Available: 5774MB
Check Python executable.............................[OK]
  Using bundled python 3.6.13 |Anaconda, Inc.| (default, Jun  4 2021, 14:25:59)
[GCC 7.5.0] at /home/audreyb/sct/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if colored is installed.......................[OK] (1.4.2)
Check if dipy is installed..........................[OK] (1.4.1)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras (2.1.5) is installed.................[OK] (2.1.5)
Check if ivadomed is installed......................Generating new fontManager, this may take some time...
[OK] (2.7.4)
Check if matplotlib is installed....................[OK] (3.3.4)
Check if nibabel is installed.......................[OK] (3.2.1)
Check if numpy is installed.........................[OK] (1.19.5)
Check if onnxruntime (1.4.0) is installed...........[OK] (1.4.0)
Check if pandas is installed........................[OK] (1.1.5)
Check if psutil is installed........................[OK] (5.8.0)
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3)
Check if pytest is installed........................[OK] (6.2.4)
Check if pytest-cov is installed....................[OK] (2.12.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.26.0)
Check if requirements-parser is installed...........[OK] (0.2.0)
Check if scipy is installed.........................[OK] (1.5.4)
Check if scikit-image is installed..................[OK] (0.17.2)
Check if scikit-learn is installed..................[OK] (0.24.2)
Check if tensorflow (1.5.0) is installed............[OK] (1.5.0)
Check if torch (1.5.0+cpu) is installed.............[OK] (1.5.0+cpu)
Check if torchvision (0.6.0+cpu) is installed.......[OK] (0.6.0+cpu)
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.62.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3 is installed.......................[OK] (1.26.6)
Check if pytest_console_scripts is installed........[OK]
Check if wquantiles is installed....................[OK] (0.4)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if figure can be opened with matplotlib.......qt.qpa.screen: QXcbConnection: Could not connect to display 127.0.0.1:0.0
Could not connect to any X display.

Installation validation Failed!


Installation failed!

Please copy the output of this Terminal (starting with the command install_sct) and upload it as a .txt attachment in a new topic on SCT's forum:

--> http://forum.spinalcordmri.org/c/sct