Problem with latest version installation

Rosella_Tro · February 26, 2020, 2:15pm

Hi. that is the output of SCT 4.1.0

rosella@vivi:~/tooboxes/spinalcordtoolbox-4.1.0$ ./install_sct


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



Checking requirements...


SCT version ......... 4.1.0
Installation type ... package
Operating system .... linux
Shell config ........ /home/rosella/.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: y

--> Crash reports will be sent to the SCT development team. Thank you!


SCT will be installed here: [/home/rosella/sct_4.1.0]

Do you agree? [y]es/[n]o: y

Copying source files from /home/rosella/tooboxes/spinalcordtoolbox-4.1.0 to /home/rosella/sct_4.1.0

.......................................................................................................................................................................................................................................................................................................................................................................................................
Installing conda...


rm -rf /home/rosella/sct_4.1.0/python


mkdir -p /home/rosella/sct_4.1.0/python


wget -O /tmp/tmp.Dogz2joH6v/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2020-02-26 15:09:22--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.200.79, 104.18.201.79, 2606:4700::6812:c84f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.200.79|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 71785000 (68M) [application/x-sh]
Saving to: ‘/tmp/tmp.Dogz2joH6v/miniconda.sh’

/tmp/tmp.Dogz2joH6v/miniconda.s 100%[=========================================================>]  68.46M  60.8MB/s   in 1.1s

2020-02-26 15:09:23 (60.8 MB/s) - ‘/tmp/tmp.Dogz2joH6v/miniconda.sh’ saved [71785000/71785000]

exit status is 0

bash /tmp/tmp.Dogz2joH6v/miniconda.sh -p /home/rosella/sct_4.1.0/python -b -f

PREFIX=/home/rosella/sct_4.1.0/python
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/rosella/sct_4.1.0/python

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - asn1crypto==1.2.0=py37_0
    - ca-certificates==2019.10.16=0
    - certifi==2019.9.11=py37_0
    - cffi==1.13.0=py37h2e261b9_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h7b6447c_0
    - conda==4.7.12=py37_0
    - cryptography==2.8=py37h1ba5d50_0
    - idna==2.8=py37_0
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.2.1=hd88cf55_4
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.1=he6710b0_1
    - openssl==1.1.1d=h7b6447c_3
    - pip==19.3.1=py37_0
    - pycosat==0.6.3=py37h14c3975_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.0.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.4=h265db76_1
    - readline==7.0=h7b6447c_5
    - requests==2.22.0=py37_0
    - ruamel_yaml==0.15.46=py37h14c3975_0
    - setuptools==41.4.0=py37_0
    - six==1.12.0=py37_0
    - sqlite==3.30.0=h7b6447c_0
    - tk==8.6.8=hbc83047_0
    - tqdm==4.36.1=py_0
    - urllib3==1.24.2=py37_0
    - wheel==0.33.6=py37_0
    - xz==5.2.4=h14c3975_4
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.2.0-py37_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py37_0
  cffi               pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.7.12-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
  idna               pkgs/main/linux-64::idna-2.8-py37_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py37_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0
  pycparser          pkgs/main/linux-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.0.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.4-h265db76_1
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  requests           pkgs/main/linux-64::requests-2.22.0-py37_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0
  setuptools         pkgs/main/linux-64::setuptools-41.4.0-py37_0
  six                pkgs/main/linux-64::six-1.12.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.36.1-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.24.2-py37_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  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


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.12
  latest version: 4.8.2

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/rosella/sct_4.1.0/python/envs/venv_sct

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2020.1.1   |                0         125 KB
    certifi-2019.11.28         |           py36_0         153 KB
    ld_impl_linux-64-2.33.1    |       h53a641e_7         568 KB
    ncurses-6.2                |       he6710b0_0         1.1 MB
    openssl-1.1.1d             |       h7b6447c_4         2.5 MB
    pip-20.0.2                 |           py36_1         1.7 MB
    python-3.6.10              |       h0371630_0        29.7 MB
    setuptools-45.2.0          |           py36_0         520 KB
    sqlite-3.31.1              |       h7b6447c_0         1.1 MB
    wheel-0.34.2               |           py36_0          51 KB
    ------------------------------------------------------------
                                           Total:        37.5 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/linux-64::certifi-2019.11.28-py36_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_0
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_4
  pip                pkgs/main/linux-64::pip-20.0.2-py36_1
  python             pkgs/main/linux-64::python-3.6.10-h0371630_0
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  setuptools         pkgs/main/linux-64::setuptools-45.2.0-py36_0
  sqlite             pkgs/main/linux-64::sqlite-3.31.1-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  wheel              pkgs/main/linux-64::wheel-0.34.2-py36_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Proceed ([y]/n)?

Downloading and Extracting Packages
python-3.6.10        | 29.7 MB   | ##################################################################################### | 100%
sqlite-3.31.1        | 1.1 MB    | ##################################################################################### | 100%
openssl-1.1.1d       | 2.5 MB    | ##################################################################################### | 100%
ncurses-6.2          | 1.1 MB    | ##################################################################################### | 100%
pip-20.0.2           | 1.7 MB    | ##################################################################################### | 100%
ld_impl_linux-64-2.3 | 568 KB    | ##################################################################################### | 100%
wheel-0.34.2         | 51 KB     | ##################################################################################### | 100%
ca-certificates-2020 | 125 KB    | ##################################################################################### | 100%
setuptools-45.2.0    | 520 KB    | ##################################################################################### | 100%
certifi-2019.11.28   | 153 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...

Collecting numpy
  Using cached numpy-1.18.1-cp36-cp36m-manylinux1_x86_64.whl (20.1 MB)
Installing collected packages: numpy
Successfully installed numpy-1.18.1
Ignoring tensorflow: markers 'platform_system == "Darwin" and "15." in platform_release' don't match your environment
Requirement already satisfied: numpy in ./python/envs/venv_sct/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.18.1)
Collecting cryptography
  Using cached cryptography-2.8-cp34-abi3-manylinux2010_x86_64.whl (2.3 MB)
Collecting dipy
  Downloading dipy-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (8.1 MB)
     |████████████████████████████████| 8.1 MB 4.1 MB/s
Collecting futures
  Using cached futures-3.1.1-py3-none-any.whl (2.8 kB)
Collecting h5py
  Using cached h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB)
Collecting Keras
  Using cached Keras-2.3.1-py2.py3-none-any.whl (377 kB)
Collecting matplotlib
  Downloading matplotlib-3.1.3-cp36-cp36m-manylinux1_x86_64.whl (13.1 MB)
     |████████████████████████████████| 13.1 MB 54.3 MB/s
Collecting nibabel
  Downloading nibabel-3.0.1-py3-none-any.whl (3.3 MB)
     |████████████████████████████████| 3.3 MB 35.5 MB/s
Collecting pandas
  Downloading pandas-1.0.1-cp36-cp36m-manylinux1_x86_64.whl (10.1 MB)
     |████████████████████████████████| 10.1 MB 72.6 MB/s
Collecting psutil
  Downloading psutil-5.7.0.tar.gz (449 kB)
     |████████████████████████████████| 449 kB 69.7 MB/s
Collecting pyqt5
  Downloading PyQt5-5.14.1-5.14.1-cp35.cp36.cp37.cp38-abi3-manylinux2014_x86_64.whl (63.5 MB)
     |████████████████████████████████| 63.5 MB 53 kB/s
Collecting pytest
  Downloading pytest-5.3.5-py3-none-any.whl (235 kB)
     |████████████████████████████████| 235 kB 32.5 MB/s
Collecting pytest-cov
  Using cached pytest_cov-2.8.1-py2.py3-none-any.whl (18 kB)
Collecting raven
  Using cached raven-6.10.0-py2.py3-none-any.whl (284 kB)
Collecting requests
  Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB)
     |████████████████████████████████| 58 kB 592 kB/s
Collecting scipy
  Downloading scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl (26.1 MB)
     |████████████████████████████████| 26.1 MB 64 kB/s
Collecting scikit-image
  Using cached scikit_image-0.16.2-cp36-cp36m-manylinux1_x86_64.whl (26.5 MB)
Collecting scikit-learn
  Downloading scikit_learn-0.22.1-cp36-cp36m-manylinux1_x86_64.whl (7.0 MB)
     |████████████████████████████████| 7.0 MB 24.6 MB/s
Collecting tensorflow
  Downloading tensorflow-2.1.0-cp36-cp36m-manylinux2010_x86_64.whl (421.8 MB)
     |████████████████████████████████| 421.8 MB 13 kB/s
Collecting xlrd
  Using cached xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
Collecting xlutils
  Using cached xlutils-2.0.0-py2.py3-none-any.whl (55 kB)
Collecting xlwt
  Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
Collecting tqdm
  Downloading tqdm-4.43.0-py2.py3-none-any.whl (59 kB)
     |████████████████████████████████| 59 kB 1.5 MB/s
Processing /home/rosella/.cache/pip/wheels/3d/3c/84/28d36677f3c760c048bd02b5a547ea0c4027770cc9cdb9af1e/transforms3d-0.3.1-cp36-none-any.whl
Collecting urllib3[secure]
  Downloading urllib3-1.25.8-py2.py3-none-any.whl (125 kB)
     |████████████████████████████████| 125 kB 37.3 MB/s
Collecting six>=1.4.1
  Using cached six-1.14.0-py2.py3-none-any.whl (10 kB)
Collecting cffi!=1.11.3,>=1.8
  Downloading cffi-1.14.0-cp36-cp36m-manylinux1_x86_64.whl (399 kB)
     |████████████████████████████████| 399 kB 25.1 MB/s
Collecting keras-preprocessing>=1.0.5
  Using cached Keras_Preprocessing-1.1.0-py2.py3-none-any.whl (41 kB)
Collecting pyyaml
  Downloading PyYAML-5.3.tar.gz (268 kB)
     |████████████████████████████████| 268 kB 33.5 MB/s
Collecting keras-applications>=1.0.6
  Using cached Keras_Applications-1.0.8-py3-none-any.whl (50 kB)
Collecting kiwisolver>=1.0.1
  Using cached kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90 kB)
Collecting cycler>=0.10
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting python-dateutil>=2.1
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
  Downloading pyparsing-2.4.6-py2.py3-none-any.whl (67 kB)
     |████████████████████████████████| 67 kB 227 kB/s
Collecting pytz>=2017.2
  Using cached pytz-2019.3-py2.py3-none-any.whl (509 kB)
Collecting PyQt5-sip<13,>=12.7
  Downloading PyQt5_sip-12.7.1-cp36-cp36m-manylinux1_x86_64.whl (252 kB)
     |████████████████████████████████| 252 kB 31.0 MB/s
Collecting importlib-metadata>=0.12; python_version < "3.8"
  Downloading importlib_metadata-1.5.0-py2.py3-none-any.whl (30 kB)
Collecting attrs>=17.4.0
  Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Collecting py>=1.5.0
  Downloading py-1.8.1-py2.py3-none-any.whl (83 kB)
     |████████████████████████████████| 83 kB 560 kB/s
Collecting wcwidth
  Downloading wcwidth-0.1.8-py2.py3-none-any.whl (17 kB)
Collecting packaging
  Downloading packaging-20.1-py2.py3-none-any.whl (36 kB)
Collecting pluggy<1.0,>=0.12
  Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting more-itertools>=4.0.0
  Downloading more_itertools-8.2.0-py3-none-any.whl (43 kB)
     |████████████████████████████████| 43 kB 302 kB/s
Collecting coverage>=4.4
  Downloading coverage-5.0.3-cp36-cp36m-manylinux1_x86_64.whl (227 kB)
     |████████████████████████████████| 227 kB 34.9 MB/s
Collecting idna<3,>=2.5
  Downloading idna-2.9-py2.py3-none-any.whl (58 kB)
     |████████████████████████████████| 58 kB 1.2 MB/s
Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests->-r requirements.txt (line 15)) (2019.11.28)
Collecting chardet<4,>=3.0.2
  Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting networkx>=2.0
  Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
Collecting pillow>=4.3.0
  Downloading Pillow-7.0.0-cp36-cp36m-manylinux1_x86_64.whl (2.1 MB)
     |████████████████████████████████| 2.1 MB 21.3 MB/s
Collecting imageio>=2.3.0
  Downloading imageio-2.8.0-py3-none-any.whl (3.3 MB)
     |████████████████████████████████| 3.3 MB 34.0 MB/s
Collecting PyWavelets>=0.4.0
  Using cached PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (4.4 MB)
Collecting joblib>=0.11
  Using cached joblib-0.14.1-py2.py3-none-any.whl (294 kB)
Processing /home/rosella/.cache/pip/wheels/7c/06/54/bc84598ba1daf8f970247f550b175aaaee85f68b4b0c5ab2c6/termcolor-1.1.0-cp36-none-any.whl
Processing /home/rosella/.cache/pip/wheels/5c/2e/7e/a1d4d4fcebe6c381f378ce7743a3ced3699feb89bcfbdadadd/gast-0.2.2-cp36-none-any.whl
Collecting astor>=0.6.0
  Using cached astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting google-pasta>=0.1.6
  Using cached google_pasta-0.1.8-py3-none-any.whl (57 kB)
Collecting protobuf>=3.8.0
  Downloading protobuf-3.11.3-cp36-cp36m-manylinux1_x86_64.whl (1.3 MB)
     |████████████████████████████████| 1.3 MB 57.8 MB/s
Collecting tensorflow-estimator<2.2.0,>=2.1.0rc0
  Downloading tensorflow_estimator-2.1.0-py2.py3-none-any.whl (448 kB)
     |████████████████████████████████| 448 kB 21.5 MB/s
Processing /home/rosella/.cache/pip/wheels/8e/28/49/fad4e7f0b9a1227708cbbee4487ac8558a7334849cb81c813d/absl_py-0.9.0-cp36-none-any.whl
Collecting tensorboard<2.2.0,>=2.1.0
  Downloading tensorboard-2.1.0-py3-none-any.whl (3.8 MB)
     |████████████████████████████████| 3.8 MB 26.5 MB/s
Requirement already satisfied: wheel>=0.26; python_version >= "3" in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorflow->-r requirements.txt (line 19)) (0.34.2)
Processing /home/rosella/.cache/pip/wheels/2c/b1/94/43d03e130b929aae7ba3f8d15cbd7bc0d1cb5bb38a5c721833/opt_einsum-3.1.0-cp36-none-any.whl
Collecting wrapt>=1.11.1
  Downloading wrapt-1.12.0.tar.gz (27 kB)
Collecting grpcio>=1.8.6
  Downloading grpcio-1.27.2-cp36-cp36m-manylinux2010_x86_64.whl (2.7 MB)
     |████████████████████████████████| 2.7 MB 20.7 MB/s
Collecting pyOpenSSL>=0.14; extra == "secure"
  Using cached pyOpenSSL-19.1.0-py2.py3-none-any.whl (53 kB)
Processing /home/rosella/.cache/pip/wheels/f2/9a/90/de94f8556265ddc9d9c8b271b0f63e57b26fb1d67a45564511/pycparser-2.19-py2.py3-none-any.whl
Requirement already satisfied: setuptools in ./python/envs/venv_sct/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->-r requirements.txt (line 7)) (45.2.0.post20200210)
Collecting zipp>=0.5
  Downloading zipp-3.0.0-py3-none-any.whl (4.8 kB)
Collecting decorator>=4.3.0
  Using cached decorator-4.4.1-py2.py3-none-any.whl (9.2 kB)
Collecting markdown>=2.6.8
  Downloading Markdown-3.2.1-py2.py3-none-any.whl (88 kB)
     |████████████████████████████████| 88 kB 1.7 MB/s
Collecting google-auth<2,>=1.6.3
  Downloading google_auth-1.11.2-py2.py3-none-any.whl (76 kB)
     |████████████████████████████████| 76 kB 1.1 MB/s
Collecting werkzeug>=0.11.15
  Downloading Werkzeug-1.0.0-py2.py3-none-any.whl (298 kB)
     |████████████████████████████████| 298 kB 36.4 MB/s
Collecting google-auth-oauthlib<0.5,>=0.4.1
  Using cached google_auth_oauthlib-0.4.1-py2.py3-none-any.whl (18 kB)
Collecting rsa<4.1,>=3.1.4
  Using cached rsa-4.0-py2.py3-none-any.whl (38 kB)
Collecting pyasn1-modules>=0.2.1
  Downloading pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
     |████████████████████████████████| 155 kB 56.5 MB/s
Collecting cachetools<5.0,>=2.0.0
  Using cached cachetools-4.0.0-py3-none-any.whl (10 kB)
Collecting requests-oauthlib>=0.7.0
  Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB)
Collecting pyasn1>=0.1.3
  Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting oauthlib>=3.0.0
  Using cached oauthlib-3.1.0-py2.py3-none-any.whl (147 kB)
Building wheels for collected packages: psutil, pyyaml, wrapt
  Building wheel for psutil (setup.py) ... done
  Created wheel for psutil: filename=psutil-5.7.0-cp36-cp36m-linux_x86_64.whl size=278731 sha256=de9602841b372b99a0574aa59dcc8dc9b34689e46c1528df8e1a63350bbd4fb7
  Stored in directory: /home/rosella/.cache/pip/wheels/a1/d9/f2/b5620c01e9b3e858c6877b1045fda5b115cf7df6490f883382
  Building wheel for pyyaml (setup.py) ... done
  Created wheel for pyyaml: filename=PyYAML-5.3-cp36-cp36m-linux_x86_64.whl size=44229 sha256=21bcb3dccddc3ceececa383934828c243e7337485013bfd1e17ea0e18458abfa
  Stored in directory: /home/rosella/.cache/pip/wheels/b1/86/0d/10e6c39d3a2b85ba807d7657ee80f08cc16c03f2aa2adf8e46
  Building wheel for wrapt (setup.py) ... done
  Created wheel for wrapt: filename=wrapt-1.12.0-cp36-cp36m-linux_x86_64.whl size=75665 sha256=e464388c9970feba67214d359cc4051482be3a054378e88562117b5e9e375641
  Stored in directory: /home/rosella/.cache/pip/wheels/d6/61/05/e03fa5094273d241c17ab2a0b774027a6e167870275e93bf25
Successfully built psutil pyyaml wrapt
Installing collected packages: six, pycparser, cffi, cryptography, h5py, nibabel, scipy, dipy, futures, keras-preprocessing, pyyaml, keras-applications, Keras, kiwisolver, cycler, python-dateutil, pyparsing, matplotlib, pytz, pandas, psutil, PyQt5-sip, pyqt5, zipp, importlib-metadata, attrs, py, wcwidth, packaging, pluggy, more-itertools, pytest, coverage, pytest-cov, raven, idna, pyOpenSSL, urllib3, chardet, requests, decorator, networkx, pillow, imageio, PyWavelets, scikit-image, joblib, scikit-learn, termcolor, gast, astor, google-pasta, protobuf, tensorflow-estimator, absl-py, grpcio, markdown, pyasn1, rsa, pyasn1-modules, cachetools, google-auth, werkzeug, oauthlib, requests-oauthlib, google-auth-oauthlib, tensorboard, opt-einsum, wrapt, tensorflow, xlrd, xlwt, xlutils, tqdm, transforms3d
Successfully installed Keras-2.3.1 PyQt5-sip-12.7.1 PyWavelets-1.1.1 absl-py-0.9.0 astor-0.8.1 attrs-19.3.0 cachetools-4.0.0 cffi-1.14.0 chardet-3.0.4 coverage-5.0.3 cryptography-2.8 cycler-0.10.0 decorator-4.4.1 dipy-1.1.1 futures-3.1.1 gast-0.2.2 google-auth-1.11.2 google-auth-oauthlib-0.4.1 google-pasta-0.1.8 grpcio-1.27.2 h5py-2.10.0 idna-2.9 imageio-2.8.0 importlib-metadata-1.5.0 joblib-0.14.1 keras-applications-1.0.8 keras-preprocessing-1.1.0 kiwisolver-1.1.0 markdown-3.2.1 matplotlib-3.1.3 more-itertools-8.2.0 networkx-2.4 nibabel-3.0.1 oauthlib-3.1.0 opt-einsum-3.1.0 packaging-20.1 pandas-1.0.1 pillow-7.0.0 pluggy-0.13.1 protobuf-3.11.3 psutil-5.7.0 py-1.8.1 pyOpenSSL-19.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pycparser-2.19 pyparsing-2.4.6 pyqt5-5.14.1 pytest-5.3.5 pytest-cov-2.8.1 python-dateutil-2.8.1 pytz-2019.3 pyyaml-5.3 raven-6.10.0 requests-2.23.0 requests-oauthlib-1.3.0 rsa-4.0 scikit-image-0.16.2 scikit-learn-0.22.1 scipy-1.4.1 six-1.14.0 tensorboard-2.1.0 tensorflow-2.1.0 tensorflow-estimator-2.1.0 termcolor-1.1.0 tqdm-4.43.0 transforms3d-0.3.1 urllib3-1.25.8 wcwidth-0.1.8 werkzeug-1.0.0 wrapt-1.12.0 xlrd-1.2.0 xlutils-2.0.0 xlwt-1.3.0 zipp-3.0.0
Obtaining file:///home/rosella/sct_4.1.0
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox

Creating launchers for Python scripts...


Make shell scripts executable...


Creating symbolic links for Shell scripts...


Installing binaries...


sct_download_data -d binaries_debian -o /home/rosella/sct_4.1.0/bin


--
Spinal Cord Toolbox (4.1.0)

Folder /home/rosella/sct_4.1.0/bin has been created.

Trying URL: https://osf.io/bt58d/?action=download
Downloading 20190930_sct_binaries_linux.tar.gz...
Status: 100%|##############################################################################| 81.1M/81.1M [00:06<00:00, 11.6MB/s]

Create temporary folder (/tmp/sct-20200226151123.255541-w8g0v5da)...

Unzip data to: /tmp/sct-20200226151123.255541-w8g0v5da

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


All requirements installed!


. /home/rosella/sct_4.1.0/python/bin/activate /home/rosella/sct_4.1.0/python


Installing data...


rm -rf /home/rosella/sct_4.1.0/data


mkdir -p /home/rosella/sct_4.1.0/data


cd /home/rosella/sct_4.1.0/data


sct_download_data -d PAM50


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/kc3jx/?action=download
Downloading 20181214_PAM50.zip...
Status: 100%|##############################################################################| 70.8M/70.8M [00:04<00:00, 17.5MB/s]

Create temporary folder (/tmp/sct-20200226151131.694202-slgw4390)...

Unzip data to: /tmp/sct-20200226151131.694202-slgw4390

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d gm_model


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/ugscu/?action=download
Downloading 20160922_gm_model.zip...
Status: 100%|##############################################################################| 10.3M/10.3M [00:00<00:00, 14.5MB/s]

Create temporary folder (/tmp/sct-20200226151134.651134-8_w90zbr)...

Unzip data to: /tmp/sct-20200226151134.651134-8_w90zbr

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d optic_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/g4fwn/?action=download
Downloading 20170413_optic_models.zip...
Status: 100%|###############################################################################| 17.7k/17.7k [00:00<00:00, 754kB/s]

Create temporary folder (/tmp/sct-20200226151136.767825-c_ijrofy)...

Unzip data to: /tmp/sct-20200226151136.767825-c_ijrofy

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d pmj_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/4gufr/?action=download
Downloading 20170922_pmj_models.zip...
Status: 100%|##############################################################################| 8.87k/8.87k [00:00<00:00, 2.91MB/s]

Create temporary folder (/tmp/sct-20200226151139.630205-0xbenq69)...

Unzip data to: /tmp/sct-20200226151139.630205-0xbenq69

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d deepseg_sc_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/avf97/?action=download
Downloading 20180610_deepseg_sc_models.zip...
Status: 100%|##############################################################################| 58.7M/58.7M [00:02<00:00, 26.4MB/s]

Create temporary folder (/tmp/sct-20200226151143.850584-1cgrt_e7)...

Unzip data to: /tmp/sct-20200226151143.850584-1cgrt_e7

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d deepseg_gm_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/b9y4x/?action=download
Downloading 20180205_deepseg_gm_models.zip...
Status: 100%|##############################################################################| 2.28M/2.28M [00:00<00:00, 5.72MB/s]

Create temporary folder (/tmp/sct-20200226151146.440101-fi82hge5)...

Unzip data to: /tmp/sct-20200226151146.440101-fi82hge5

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d deepseg_lesion_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/eg7v9/?action=download
Downloading 20180613_deepseg_lesion_models.zip...
Status: 100%|##############################################################################| 16.0M/16.0M [00:00<00:00, 19.3MB/s]

Create temporary folder (/tmp/sct-20200226151150.338698-0w5oynjg)...

Unzip data to: /tmp/sct-20200226151150.338698-0w5oynjg

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d c2c3_disc_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/t97ap/?action=download
Downloading 20190117_c2c3_disc_models.zip...
Status: 100%|##############################################################################| 8.94k/8.94k [00:00<00:00, 14.1MB/s]

Create temporary folder (/tmp/sct-20200226151152.671078-ggk2t0ji)...

Unzip data to: /tmp/sct-20200226151152.671078-ggk2t0ji

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


In case an old version SCT is already installed (4.0.0-beta.1 or before), remove 'sct_env' declaration in RC file


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


Validate installation...


--
Spinal Cord Toolbox (4.1.0)

SCT info:
- version: 4.1.0
- path: /home/rosella/sct_4.1.0
OS: linux (Linux-3.16.0-4-amd64-x86_64-with-debian-bullseye-sid)
CPU cores: Available: 8, Used by SCT: 8
RAM: MemTotal:       32970652 kB
total       used       free     shared    buffers     cached
Mem:         32197      10832      21365         40       1027       7949
-/+ buffers/cache:       1855      30342
Swap:        57218          0      57218
Check Python executable.............................[OK]
  Using bundled python 3.6.10 |Anaconda, Inc.| (default, Jan  7 2020, 21:14:29)
[GCC 7.3.0] at /home/rosella/sct_4.1.0/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.18.1)
Check if cryptography is installed..................[OK] (2.8)
Check if dipy is installed..........................[OK] (1.1.1)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras is installed.........................2020-02-26 15:12:09.525815: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'libnvinfer.so.6'; dlerror: libnvinfer.so.6: cannot open shared object file: No such file or directory
2020-02-26 15:12:09.525910: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'libnvinfer_plugin.so.6'; dlerror: libnvinfer_plugin.so.6: cannot open shared object file: No such file or directory
2020-02-26 15:12:09.525924: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:30] Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
[OK] (2.3.1)
Check if matplotlib is installed....................[OK] (3.1.3)
Check if nibabel is installed.......................[OK] (3.0.1)
Check if pandas is installed........................[OK] (1.0.1)
Check if psutil is installed........................[OK] (5.7.0)
Check if pyqt5 is installed.........................[OK]
Check if pytest is installed........................[OK] (5.3.5)
Check if pytest-cov is installed....................[OK] (2.8.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.23.0)
Check if scipy is installed.........................[OK] (1.4.1)
Check if scikit-image is installed..................[OK] (0.16.2)
Check if scikit-learn is installed..................[OK] (0.22.1)
Check if tensorflow is installed....................[OK] (2.1.0)
Check if xlrd is installed..........................[OK] (1.2.0)
Check if xlutils is installed.......................[OK]
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.43.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.8)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if figure can be opened.......................[OK]


Open a new Terminal window to load environment variables, or run:
source /home/rosella/.bashrc


Installation finished successfully!

jcohenadad · February 26, 2020, 2:32pm

Thank you for the feedback Rosella,
To make sure SCT works with all the functions, could you please also run the following:

sct_testing

And send us the Terminal output (p.s. you can use “~~~” before and after the copy/pasted code for a nice formatting)

Rosella_Tro · February 26, 2020, 2:50pm

rosella@vivi:~$ sct_testing

--
Spinal Cord Toolbox (4.2.1)

Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 8 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_convert sct_compute_ernst_angle sct_compute_hausdorff_distance sct_compute_mtr sct_compute_mscc sct_compute_snr sct_concat_transfo sct_create_mask sct_crop_image sct_dice_coefficient sct_detect_pmj sct_dmri_compute_dti sct_dmri_concat_b0_and_dwi sct_dmri_concat_bvals sct_dmri_concat_bvecs sct_dmri_create_noisemask sct_dmri_compute_bvalue sct_dmri_moco sct_dmri_separate_b0_and_dwi sct_dmri_transpose_bvecs sct_extract_metric sct_flatten_sagittal sct_fmri_compute_tsnr sct_fmri_moco sct_get_centerline sct_image sct_label_utils sct_label_vertebrae sct_maths sct_merge_images sct_process_segmentation sct_propseg sct_qc sct_register_multimodal sct_register_to_template sct_resample sct_smooth_spinalcord sct_straighten_spinalcord sct_warp_template
Checking sct_deepseg_gm.............................[OK]
Checking sct_deepseg_lesion.........................[OK]
Checking sct_deepseg_sc.............................[OK]
Checking sct_analyze_lesion.........................[OK]
Checking sct_analyze_texture........................[OK]
Checking sct_apply_transfo..........................[OK]
Checking sct_convert................................[OK]
Checking sct_compute_ernst_angle....................[OK]
Checking sct_compute_hausdorff_distance.............[OK]
Checking sct_compute_mtr............................[OK]
Checking sct_compute_mscc...........................[OK]
Checking sct_compute_snr............................[OK]
Checking sct_concat_transfo.........................[OK]
Checking sct_create_mask............................[OK]
Checking sct_crop_image.............................[OK]
Checking sct_dice_coefficient.......................[OK]
Checking sct_detect_pmj.............................[OK]
Checking sct_dmri_compute_dti.......................[OK]
Checking sct_dmri_concat_b0_and_dwi.................[OK]
Checking sct_dmri_concat_bvals......................[OK]
Checking sct_dmri_concat_bvecs......................[OK]
Checking sct_dmri_create_noisemask..................[OK]
Checking sct_dmri_compute_bvalue....................[OK]
Checking sct_dmri_moco..............................[OK]
Checking sct_dmri_separate_b0_and_dwi...............[OK]
Checking sct_dmri_transpose_bvecs...................[OK]
Checking sct_extract_metric.........................[OK]
Checking sct_flatten_sagittal.......................[OK]
Checking sct_fmri_compute_tsnr......................[OK]
Checking sct_fmri_moco..............................[OK]
Checking sct_get_centerline.........................[OK]
Checking sct_image..................................[OK]
Checking sct_label_utils............................[OK]
Checking sct_label_vertebrae........................[FAIL]

   ====================================================================================================
   sct_label_vertebrae -i t2/t2.nii.gz -s t2/t2_seg.nii.gz -c t2 -initfile t2/init_label_vertebrae.txt -t template -qc testing-qc
   ====================================================================================================


   --
   Spinal Cord Toolbox (4.2.1)

   Folder testing-qc has been created.

   Create temporary folder (/tmp/sct-20200226154157.985916-label_vertebrae-d4yad18i)...

   Copying input data to tmp folder...

   Straighten spinal cord...
   Reusing existing warping field which seems to be valid
   cp /home/rosella/sct_testing_data/warp_curve2straight.nii.gz warp_curve2straight.nii.gz
   cp /home/rosella/sct_testing_data/warp_straight2curve.nii.gz warp_straight2curve.nii.gz
   cp /home/rosella/sct_testing_data/straight_ref.nii.gz straight_ref.nii.gz
   sct_apply_transfo -i data.nii -w warp_curve2straight.nii.gz -d straight_ref.nii.gz -o data_straight.nii # in /tmp/sct-20200226154157.985916-label_vertebrae-d4yad18i

   Resample to 0.5mm isotropic...
   sct_resample -i data_straight.nii -mm 0.5x0.5x0.5 -x linear -o data_straightr.nii # in /tmp/sct-20200226154157.985916-label_vertebrae-d4yad18i

   Apply straightening to segmentation...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -r data_straightr.nii -t warp_curve2straight.nii.gz -o segmentation_straight.nii -n Linear # in /tmp/sct-20200226154157.985916-label_vertebrae-d4yad18i
   sct_maths -i segmentation_straight.nii -thr 0.5 -o segmentation_straight.nii # in /tmp/sct-20200226154157.985916-label_vertebrae-d4yad18i

   Create label to identify disc...
   Label #0: 26,29,34 --> 3
   WARNING: File /tmp/sct-20200226154157.985916-label_vertebrae-d4yad18i/labelz.nii.gz already exists. Will overwrite it.

   Done! To view results, type:
   fsleyes /tmp/sct-20200226154157.985916-label_vertebrae-d4yad18i/labelz.nii.gz &


   And apply straightening to label...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i labelz.nii.gz -r data_straightr.nii -t warp_curve2straight.nii.gz -o labelz_straight.nii.gz -n NearestNeighbor # in /tmp/sct-20200226154157.985916-label_vertebrae-d4yad18i

   Get z and disc values from straight label...
   .. [68, 3]

   Look for template...
   Path template: /home/rosella/sct_testing_data/template
   Traceback (most recent call last):
   File "/home/rosella/sct_4.2.1/scripts/sct_label_vertebrae.py", line 427, in <module>
   main()
   File "/home/rosella/sct_4.2.1/scripts/sct_label_vertebrae.py", line 372, in main
   verbose=verbose, path_template=path_template, path_output=path_output, scale_dist=scale_dist)
   File "/home/rosella/sct_4.2.1/spinalcordtoolbox/vertebrae/core.py", line 68, in vertebral_detection
   fname_template = get_file_label(os.path.join(path_template, 'template'), id_label=id_label_dct[contrast.upper()], output='filewithpath')  # label = *-weighted template
   File "/home/rosella/sct_4.2.1/spinalcordtoolbox/metadata.py", line 212, in get_file_label
   raise RuntimeError("Label ID {} not found in {}".format(id_label, fname_label))
   RuntimeError: Label ID 1 not found in /home/rosella/sct_testing_data/template/template/info_label.txt

   ====================================================================================================
   sct_label_vertebrae -i t2/t2.nii.gz -s t2/t2_seg.nii.gz -c t2 -discfile t2/labels.nii.gz
   ====================================================================================================


   --
   Spinal Cord Toolbox (4.2.1)


   Create temporary folder (/tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f)...

   Copying input data to tmp folder...

   Straighten spinal cord...
   Reusing existing warping field which seems to be valid
   cp /home/rosella/sct_testing_data/warp_curve2straight.nii.gz warp_curve2straight.nii.gz
   cp /home/rosella/sct_testing_data/warp_straight2curve.nii.gz warp_straight2curve.nii.gz
   cp /home/rosella/sct_testing_data/straight_ref.nii.gz straight_ref.nii.gz
   sct_apply_transfo -i data.nii -w warp_curve2straight.nii.gz -d straight_ref.nii.gz -o data_straight.nii # in /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f

   Resample to 0.5mm isotropic...
   sct_resample -i data_straight.nii -mm 0.5x0.5x0.5 -x linear -o data_straightr.nii # in /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f

   Apply straightening to segmentation...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -r data_straightr.nii -t warp_curve2straight.nii.gz -o segmentation_straight.nii -n Linear # in /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f
   sct_maths -i segmentation_straight.nii -thr 0.5 -o segmentation_straight.nii # in /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f

   Apply straightening to disc labels...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i /home/rosella/sct_testing_data/t2/labels.nii.gz -r data_straightr.nii -t warp_curve2straight.nii.gz -o labeldisc_straight.nii.gz -n NearestNeighbor # in /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f

   Un-straighten labeling...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i segmentation_straight_labeled.nii -r segmentation.nii -t warp_straight2curve.nii.gz -o segmentation_labeled.nii -n NearestNeighbor # in /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f

   Clean labeled segmentation (correct interpolation errors)...
   WARNING: File /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f/segmentation_labeled.nii already exists. Will overwrite it.

   Label discs...

   Generate output files...
   WARNING: File ./t2_seg_labeled.nii.gz already exists. Deleting it...
   sct_convert -i /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f/segmentation_labeled.nii -o ./t2_seg_labeled.nii.gz
   File created: ./t2_seg_labeled.nii.gz
   WARNING: File ./t2_seg_labeled_discs.nii.gz already exists. Deleting it...
   sct_convert -i /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f/segmentation_labeled_disc.nii -o ./t2_seg_labeled_discs.nii.gz
   File created: ./t2_seg_labeled_discs.nii.gz
   WARNING: File ./warp_curve2straight.nii.gz already exists. Deleting it...
   File created: ./warp_curve2straight.nii.gz
   WARNING: File ./warp_straight2curve.nii.gz already exists. Deleting it...
   File created: ./warp_straight2curve.nii.gz
   WARNING: File ./straight_ref.nii.gz already exists. Deleting it...
   File created: ./straight_ref.nii.gz

   Remove temporary files...
   rm -rf /tmp/sct-20200226154204.018783-label_vertebrae-x6lev80f

   Done! To view results, type:
   fsleyes /home/rosella/sct_testing_data/t2/t2.nii.gz -a 100.0 ./t2_seg_labeled.nii.gz -cm subcortical -a 50.0 &

   ====================================================================================================
   INTEGRITY TESTING
   ====================================================================================================


   Not implemented.
Checking sct_maths..................................[OK]
Checking sct_merge_images...........................[OK]
Checking sct_process_segmentation...................[OK]
Checking sct_propseg................................[OK]
Checking sct_qc.....................................[OK]
Checking sct_register_multimodal....................[OK]
Checking sct_register_to_template...................[FAIL]

   ====================================================================================================
   sct_register_to_template -i t2/t2.nii.gz -s t2/t2_seg.nii.gz -l t2/labels.nii.gz -param step=1,type=seg,algo=centermassrot,metric=MeanSquares:step=2,type=seg,algo=bsplinesyn,iter=5,metric=MeanSquares -t template -qc qc-testing
   ====================================================================================================


   --
   Spinal Cord Toolbox (4.2.1)

   Folder qc-testing has been created.
   Traceback (most recent call last):
   File "/home/rosella/sct_4.2.1/scripts/sct_register_to_template.py", line 807, in <module>
   main()
   File "/home/rosella/sct_4.2.1/scripts/sct_register_to_template.py", line 265, in main
   file_template = get_file_label(os.path.join(path_template, 'template'), id_label=id_label_dct[contrast_template.upper()])  # label = *-weighted template
   File "/home/rosella/sct_4.2.1/spinalcordtoolbox/metadata.py", line 212, in get_file_label
   raise RuntimeError("Label ID {} not found in {}".format(id_label, fname_label))
   RuntimeError: Label ID 1 not found in template/template/info_label.txt

   ====================================================================================================
   sct_register_to_template -i t2/t2.nii.gz -s t2/t2_seg.nii.gz -ldisc t2/labels.nii.gz -ref subject
   ====================================================================================================


   --
   Spinal Cord Toolbox (4.2.1)

   Estimate cord angle for each slice:   0%|                                  | 0/55 [00:00<?, ?iter/s]
   Estimate cord angle for each slice:  11%|██▊                       | 6/55 [00:00<00:00, 59.82iter/s]
   Estimate cord angle for each slice:  35%|████████▋                | 19/55 [00:00<00:00, 70.58iter/s]
   Estimate cord angle for each slice:  64%|███████████████▉         | 35/55 [00:00<00:00, 84.78iter/s]
   Estimate cord angle for each slice:  95%|███████████████████████▋ | 52/55 [00:00<00:00, 99.50iter/s]
   Estimate cord angle for each slice: 100%|████████████████████████| 55/55 [00:00<00:00, 128.66iter/s]
   Build 3D deformation field:   0%|                                          | 0/55 [00:00<?, ?iter/s]
   Build 3D deformation field:  11%|███▋                              | 6/55 [00:00<00:00, 53.60iter/s]
   Build 3D deformation field:  18%|██████                           | 10/55 [00:00<00:00, 47.43iter/s]
   Build 3D deformation field:  29%|█████████▌                       | 16/55 [00:00<00:00, 49.76iter/s]
   Build 3D deformation field:  40%|█████████████▏                   | 22/55 [00:00<00:00, 51.81iter/s]
   Build 3D deformation field:  51%|████████████████▊                | 28/55 [00:00<00:00, 53.36iter/s]
   Build 3D deformation field:  62%|████████████████████▍            | 34/55 [00:00<00:00, 54.53iter/s]
   Build 3D deformation field:  73%|████████████████████████         | 40/55 [00:00<00:00, 55.34iter/s]
   Build 3D deformation field:  84%|███████████████████████████▌     | 46/55 [00:00<00:00, 55.81iter/s]
   Build 3D deformation field:  95%|███████████████████████████████▏ | 52/55 [00:00<00:00, 56.26iter/s]
   Build 3D deformation field: 100%|█████████████████████████████████| 55/55 [00:01<00:00, 54.62iter/s]
   Check template files...
   OK: /home/rosella/sct_4.2.1/data/PAM50/template/PAM50_t2.nii.gz
   OK: /home/rosella/sct_4.2.1/data/PAM50/template/PAM50_levels.nii.gz
   OK: /home/rosella/sct_4.2.1/data/PAM50/template/PAM50_cord.nii.gz

   Check parameters:
   Data:                 t2/t2.nii.gz
   Landmarks:            t2/labels.nii.gz
   Segmentation:         t2/t2_seg.nii.gz
   Path template:        /home/rosella/sct_4.2.1/data/PAM50
   Remove temp files:    1

   Check input labels...

   Create temporary folder (/tmp/sct-20200226154206.779172-register_to_template-60y0kbpl)...

   Copying input data to tmp folder and convert to nii...
   WARNING: File /tmp/sct-20200226154206.779172-register_to_template-60y0kbpl/template_label.nii.gz already exists. Will overwrite it.

   Check if provided labels are available in the template

   Binarize segmentation

   Done! To view results, type:
   fsleyes seg_bin.nii.gz &


   Change orientation of input images to RPI...

   Remove unused label on template. Keep only label present in the input label image...
   sct_label_utils -i template_label.nii.gz -o template_label.nii.gz -remove-reference /tmp/sct-20200226154206.779172-register_to_template-60y0kbpl/label_projected_rpi.nii.gz # in /tmp/sct-20200226154206.779172-register_to_template-60y0kbpl
   WARNING: File /tmp/sct-20200226154206.779172-register_to_template-60y0kbpl/label_projected_rpi.nii.gz already exists. Will overwrite it.
   WARNING: File /tmp/sct-20200226154206.779172-register_to_template-60y0kbpl/template_label.nii.gz already exists. Will overwrite it.

   Create temporary folder (/tmp/sct-20200226154212.995768-register-k5r630on)...

   Copying input data to tmp folder and convert to nii...

   --
   ESTIMATE TRANSFORMATION FOR STEP #0
   Registration parameters:
   type ........... label
   algo ........... syn
   slicewise ...... 0
   metric ......... MeanSquares
   iter ........... 10
   smooth ......... 0
   laplacian ...... 0
   shrink ......... 1
   gradStep ....... 0.5
   deformation .... 1x1x0
   init ...........
   poly ........... 5
   filter_size .... 5
   dof ............ Tx_Ty_Tz_Rx_Ry_Rz_Sz
   smoothWarpXY ... 2
   rot_method ..... pca
   Labels src: [[-0.0, 46.220001220703125, -107.84002685546875], [-0.0, 46.220001220703125, -144.84002685546875], [5.0, 46.220001220703125, -107.84002685546875]]
   Labels dest: [[7.2192840576171875, -1.7866058349609375, 24.678329467773438], [7.2192840576171875, -0.7866058349609375, -10.321670532226562], [12.219284057617188, -1.7866058349609375, 24.678329467773438]]
   Degrees of freedom (dof): Tx_Ty_Tz_Rx_Ry_Rz_Sz
   Optimization terminated successfully.
   Current function value: 0.000000
   Iterations: 8
   Function evaluations: 870
   Matrix:
   [[ 1.00000000e+00 -1.11442507e-12 -9.53408633e-14]
   [ 1.11669340e-12  9.99592086e-01  2.85597739e-02]
   [ 6.34742443e-14 -2.85597739e-02  9.99592086e-01]]
   Center:
   [ 8.88595072 -1.4532725  13.0116628 ]
   Translation:
   [[  -7.21928406   47.67327372 -133.18502299]]

   --
   ESTIMATE TRANSFORMATION FOR STEP #1

   Apply transformation from previous step

   Parse list of warping fields...

   Get dimensions of data...
   141 x 141 x 991 x 1

   Apply transformation...

   Apply transformation and resample to destination space...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_0.txt -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20200226154212.995768-register-k5r630on
   Copy affine matrix from destination space to make sure qform/sform are the same.
   WARNING: the resulting image could have wrong apparent results. You should use an affine transformation as last transformation...

   Done! To view results, type:
   fsleyes dest_RPI.nii src_reg.nii &


   Parse list of warping fields...

   Get dimensions of data...
   141 x 141 x 991 x 1

   Apply transformation...

   Apply transformation and resample to destination space...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_0.txt -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20200226154212.995768-register-k5r630on
   Copy affine matrix from destination space to make sure qform/sform are the same.
   WARNING: the resulting image could have wrong apparent results. You should use an affine transformation as last transformation...

   Done! To view results, type:
   fsleyes dest_seg_RPI.nii src_seg_reg.nii &

   Registration parameters:
   type ........... imseg
   algo ........... centermassrot
   slicewise ...... 0
   metric ......... MeanSquares
   iter ........... 10
   smooth ......... 0
   laplacian ...... 0
   shrink ......... 1
   gradStep ....... 0.5
   deformation .... 1x1x0
   init ...........
   poly ........... 5
   filter_size .... 5
   dof ............ Tx_Ty_Tz_Rx_Ry_Rz
   smoothWarpXY ... 2
   rot_method ..... pcahog

   Create temporary folder (/tmp/sct-20200226154216.417014-register-tzc546hh)...

   Copy input data to temp folder...
   sct_convert -i src_reg.nii -o /tmp/sct-20200226154216.417014-register-tzc546hh/src.nii
   sct_convert -i src_seg_reg.nii -o /tmp/sct-20200226154216.417014-register-tzc546hh/src_seg.nii
   sct_convert -i dest_RPI.nii -o /tmp/sct-20200226154216.417014-register-tzc546hh/dest.nii
   sct_convert -i dest_seg_RPI.nii -o /tmp/sct-20200226154216.417014-register-tzc546hh/dest_seg.nii

   Get image dimensions of destination image...
   matrix size: 52 x 60 x 55
   voxel size:  1.0mm x 1.0mm x 1.0mm

   Split input segmentation...

   Split destination segmentation...

   Split input image...

   Split destination image...

   Generate warping field...
   --> step1Warp.nii.gz

   Generate warping field...
   --> step1InverseWarp.nii.gz

   Move warping fields...
   cp step1Warp.nii.gz /tmp/sct-20200226154212.995768-register-k5r630on
   cp step1InverseWarp.nii.gz /tmp/sct-20200226154212.995768-register-k5r630on
   rm -rf /tmp/sct-20200226154216.417014-register-tzc546hh

   --
   ESTIMATE TRANSFORMATION FOR STEP #2

   Apply transformation from previous step

   Parse list of warping fields...

   Get dimensions of data...
   141 x 141 x 991 x 1

   Apply transformation...

   Apply transformation and resample to destination space...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz warp_forward_0.txt -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20200226154212.995768-register-k5r630on
   Copy affine matrix from destination space to make sure qform/sform are the same.

   Done! To view results, type:
   fsleyes dest_seg_RPI.nii src_seg_reg.nii &

   Registration parameters:
   type ........... seg
   algo ........... bsplinesyn
   slicewise ...... 0
   metric ......... MeanSquares
   iter ........... 3
   smooth ......... 1
   laplacian ...... 0
   shrink ......... 1
   gradStep ....... 0.5
   deformation .... 1x1x0
   init ...........
   poly ........... 5
   filter_size .... 5
   dof ............ Tx_Ty_Tz_Rx_Ry_Rz
   smoothWarpXY ... 2
   rot_method ..... pca
   sct_image -i dest_seg_RPI.nii -o dest_seg_RPI_pad.nii -pad 0,0,10 # in /tmp/sct-20200226154212.995768-register-k5r630on

   Estimate transformation
   /home/rosella/sct_4.2.1/bin/isct_antsRegistration --dimensionality 3 --transform 'bsplinesyn[0.5,1,3]' --metric 'MeanSquares[dest_seg_RPI_pad.nii,src_seg_reg.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 1mm --restrict-deformation 1x1x0 --output '[step2,src_seg_reg_regStep2.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20200226154212.995768-register-k5r630on

   Concatenate transformations...

   Parse list of warping fields...

   Check file existence...
   OK: dest.nii
   OK: warp_forward_0.txt
   OK: warp_forward_1.nii.gz
   OK: warp_forward_2.nii.gz
   /home/rosella/sct_4.2.1/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz warp_forward_0.txt # in /tmp/sct-20200226154212.995768-register-k5r630on

   Generate output files...
   File created: warp_src2dest.nii.gz

   Parse list of warping fields...

   Check file existence...
   OK: src.nii
   OK: warp_inverse_2.nii.gz
   OK: warp_inverse_1.nii.gz
   OK: warp_forward_0.txt
   /home/rosella/sct_4.2.1/bin/isct_ComposeMultiTransform 3 warp_final.nii.gz -R src.nii -i warp_forward_0.txt warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /tmp/sct-20200226154212.995768-register-k5r630on

   Generate output files...
   File created: warp_dest2src.nii.gz


   Apply transfo source --> dest...

   Parse list of warping fields...

   Get dimensions of data...
   141 x 141 x 991 x 1

   Apply transformation...

   Apply transformation and resample to destination space...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /tmp/sct-20200226154212.995768-register-k5r630on
   Copy affine matrix from destination space to make sure qform/sform are the same.

   Done! To view results, type:
   fsleyes dest.nii src_reg.nii &


   Apply transfo dest --> source...

   Parse list of warping fields...

   Get dimensions of data...
   52 x 60 x 55 x 1

   Apply transformation...

   Apply transformation and resample to destination space...
   /home/rosella/sct_4.2.1/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /tmp/sct-20200226154212.995768-register-k5r630on
   Copy affine matrix from destination space to make sure qform/sform are the same.

   Done! To view results, type:
   fsleyes src.nii dest_reg.nii &


   Generate output files...
   File created: template_reg.nii
   File created: data_rpi_reg.nii
   File created: warp_template2data_rpi.nii.gz
   File created: warp_data_rpi2template.nii.gz

   Remove temporary files...
   rm -rf /tmp/sct-20200226154212.995768-register-k5r630on
   sct_apply_transfo -i template.nii -o template2anat.nii.gz -d data.nii -w warp_template2anat.nii.gz -crop 0 # in /tmp/sct-20200226154206.779172-register_to_template-60y0kbpl
   sct_apply_transfo -i data.nii -o anat2template.nii.gz -d template.nii -w warp_anat2template.nii.gz -crop 0 # in /tmp/sct-20200226154206.779172-register_to_template-60y0kbpl

   Generate output files...
   WARNING: File warp_template2anat.nii.gz already exists. Deleting it...
   File created: warp_template2anat.nii.gz
   WARNING: File warp_anat2template.nii.gz already exists. Deleting it...
   File created: warp_anat2template.nii.gz
   WARNING: File template2anat.nii.gz already exists. Deleting it...
   File created: template2anat.nii.gz
   WARNING: File anat2template.nii.gz already exists. Deleting it...
   File created: anat2template.nii.gz

   Delete temporary files...
   rm -rf /tmp/sct-20200226154206.779172-register_to_template-60y0kbpl

   Finished! Elapsed time: 33s

   Done! To view results, type:
   fsleyes t2/t2.nii.gz template2anat.nii.gz &


   Done! To view results, type:
   fsleyes /home/rosella/sct_4.2.1/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz &

   ====================================================================================================
   INTEGRITY TESTING
   ====================================================================================================

   Dice[seg,template_seg_reg]: 0.970088122129825
   --> PASSED

   Dice[seg_reg,template_seg]: 0.9427385120689121
   --> PASSED
Checking sct_resample...............................[OK]
Checking sct_smooth_spinalcord......................[OK]
Checking sct_straighten_spinalcord..................[OK]
Checking sct_warp_template..........................[OK]
status: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]
Failures: sct_label_vertebrae sct_register_to_template
Finished! Elapsed time: 86s

jcohenadad · February 26, 2020, 3:11pm

Hi Rosella,

The errors in sct_label_vertebrae and sct_register_to_template are likely related to the fact that there are now two installations of SCT on your station. You just installed SCT 4.1.0, but the sct_testing results shown above are using SCT 4.2.1. The two installations should not be mixed.

After you install SCT, you always need to start a new Terminal.

Could you please start a new Terminal and re-run (-d 1 to force download of data):

sct_testing -d 1

Rosella_Tro · February 26, 2020, 4:14pm

I found another error when trying to erode an image:
rosella@vivi:~/spinal_cord/1$ sct_maths -i kurtosis_crop_moco_dwi_mean.nii -erode 3,3,3 -o thr_seg.nii

–
Spinal Cord Toolbox (4.1.0)

Traceback (most recent call last):
File “/home/rosella/sct_4.1.0/scripts/sct_maths.py”, line 774, in
main()
File “/home/rosella/sct_4.1.0/scripts/sct_maths.py”, line 342, in main
data_out = erode(data, convert_list_str(arguments.erode))
TypeError: convert_list_str() missing 1 required positional argument: ‘type’

Rosella_Tro · February 26, 2020, 4:15pm

rosella@vivi:~$ sct_testing -d 1

--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/z8gaj/?action=download
Downloading 20180125_sct_testing_data.zip...
Status: 100%|####################################################################| 6.78M/6.78M [00:00<00:00, 7.22MB/s]

Create temporary folder (/tmp/sct-20200226171013.159120-rnaxjqaz)...

Unzip data to: /tmp/sct-20200226171013.159120-rnaxjqaz

Check if folder already exists on the destination path...
Folder sct_testing_data already exists. Removing it...

Remove temporary folders...
Done!

Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 8 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_convert sct_compute_ernst_angle sct_compute_hausdorff_distance sct_compute_mtr sct_compute_mscc sct_compute_snr sct_concat_transfo sct_create_mask sct_crop_image sct_dice_coefficient sct_detect_pmj sct_dmri_compute_dti sct_dmri_concat_b0_and_dwi sct_dmri_concat_bvals sct_dmri_concat_bvecs sct_dmri_create_noisemask sct_dmri_compute_bvalue sct_dmri_moco sct_dmri_separate_b0_and_dwi sct_dmri_transpose_bvecs sct_extract_metric sct_flatten_sagittal sct_fmri_compute_tsnr sct_fmri_moco sct_get_centerline sct_image sct_label_utils sct_label_vertebrae sct_maths sct_merge_images sct_process_segmentation sct_propseg sct_qc sct_register_multimodal sct_register_to_template sct_resample sct_smooth_spinalcord sct_straighten_spinalcord sct_warp_template
Checking sct_deepseg_gm.............................[OK]
Checking sct_deepseg_lesion.........................[FAIL]

   ====================================================================================================
   sct_deepseg_lesion -i t2/t2.nii.gz -c t2
   ====================================================================================================


   --
   Spinal Cord Toolbox (4.1.0)

   2020-02-26 17:10:25.615796: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'libnvinfer.so.6'; dlerror: libnvinfer.so.6: cannot open shared object file: No such file or directory
   2020-02-26 17:10:25.615850: W tensorflow/stream_executor/platform/default/dso_loader.cc:55] Could not load dynamic library 'libnvinfer_plugin.so.6'; dlerror: libnvinfer_plugin.so.6: cannot open shared object file: No such file or directory
   2020-02-26 17:10:25.615856: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:30] Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.

   Method:
   Centerline algorithm: svm
   Assumes brain section included in the image: True


   Create temporary folder (/tmp/sct-20200226171026.429946-5nmoucma)...
   Reorient the image to RPI, if necessary...

   Finding the spinal cord centerline...
   Remove temporary files...
   rm -rf /tmp/sct-20200226171026.679830-qoht8lru

   Cropping the image around the spinal cord...
   Normalizing the intensity...
   load data...

   Segmenting the MS lesions using deep learning on 3D patches...
   Traceback (most recent call last):
   File "/home/rosella/sct_4.1.0/scripts/sct_deepseg_lesion.py", line 178, in <module>
   main()
   File "/home/rosella/sct_4.1.0/scripts/sct_deepseg_lesion.py", line 154, in main
   brain_bool=brain_bool, remove_temp_files=remove_temp_files, verbose=verbose)
   File "/home/rosella/sct_4.1.0/spinalcordtoolbox/deepseg_lesion/core.py", line 197, in deep_segmentation_MSlesion
   im=im_res3d.copy())
   File "/home/rosella/sct_4.1.0/spinalcordtoolbox/deepseg_lesion/core.py", line 85, in segment_3d
   seg_model = load_trained_model(model_fname)
   File "/home/rosella/sct_4.1.0/spinalcordtoolbox/deepseg_sc/cnn_models_3d.py", line 94, in load_trained_model
   return load_model(model_file, custom_objects=custom_objects)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/engine/saving.py", line 492, in load_wrapper
   return load_function(*args, **kwargs)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/engine/saving.py", line 584, in load_model
   model = _deserialize_model(h5dict, custom_objects, compile)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/engine/saving.py", line 274, in _deserialize_model
   model = model_from_config(model_config, custom_objects=custom_objects)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/engine/saving.py", line 627, in model_from_config
   return deserialize(config, custom_objects=custom_objects)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/layers/__init__.py", line 168, in deserialize
   printable_module_name='layer')
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/generic_utils.py", line 147, in deserialize_keras_object
   list(custom_objects.items())))
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/engine/network.py", line 1075, in from_config
   process_node(layer, node_data)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/engine/network.py", line 1025, in process_node
   layer(unpack_singleton(input_tensors), **kwargs)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 75, in symbolic_fn_wrapper
   return func(*args, **kwargs)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/engine/base_layer.py", line 489, in __call__
   output = self.call(inputs, **kwargs)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/layers/convolutional.py", line 179, in call
   dilation_rate=self.dilation_rate)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 3965, in conv3d
   x, tf_data_format = _preprocess_conv3d_input(x, data_format)
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 3597, in _preprocess_conv3d_input
   if not _has_nchw_support():
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 522, in _has_nchw_support
   gpus_available = len(_get_available_gpus()) > 0
   File "/home/rosella/sct_4.1.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 506, in _get_available_gpus
   _LOCAL_DEVICES = tf.config.experimental_list_devices()
   AttributeError: module 'tensorflow_core._api.v2.config' has no attribute 'experimental_list_devices'
Checking sct_deepseg_sc.............................[OK]
Checking sct_analyze_lesion.........................[OK]
Checking sct_analyze_texture........................[OK]
Checking sct_apply_transfo..........................[OK]
Checking sct_convert................................[OK]
Checking sct_compute_ernst_angle....................[OK]
Checking sct_compute_hausdorff_distance.............[OK]
Checking sct_compute_mtr............................[OK]
Checking sct_compute_mscc...........................[OK]
Checking sct_compute_snr............................[OK]
Checking sct_concat_transfo.........................[OK]
Checking sct_create_mask............................[OK]
Checking sct_crop_image.............................[OK]
Checking sct_dice_coefficient.......................[OK]
Checking sct_detect_pmj.............................[OK]
Checking sct_dmri_compute_dti.......................[OK]
Checking sct_dmri_concat_b0_and_dwi.................[OK]
Checking sct_dmri_concat_bvals......................[OK]
Checking sct_dmri_concat_bvecs......................[OK]
Checking sct_dmri_create_noisemask..................[OK]
Checking sct_dmri_compute_bvalue....................[OK]
Checking sct_dmri_moco..............................[OK]
Checking sct_dmri_separate_b0_and_dwi...............[OK]
Checking sct_dmri_transpose_bvecs...................[OK]
Checking sct_extract_metric.........................[OK]
Checking sct_flatten_sagittal.......................[OK]
Checking sct_fmri_compute_tsnr......................[OK]
Checking sct_fmri_moco..............................[OK]
Checking sct_get_centerline.........................[OK]
Checking sct_image..................................[OK]
Checking sct_label_utils............................[OK]
Checking sct_label_vertebrae........................[OK]
Checking sct_maths..................................[OK]
Checking sct_merge_images...........................[OK]
Checking sct_process_segmentation...................[OK]
Checking sct_propseg................................[OK]
Checking sct_qc.....................................[OK]
Checking sct_register_multimodal....................[OK]
Checking sct_register_to_template...................[OK]
Checking sct_resample...............................[OK]
Checking sct_smooth_spinalcord......................[OK]
Checking sct_straighten_spinalcord..................[OK]
Checking sct_warp_template..........................[OK]
status: [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
Failures: sct_deepseg_lesion
Finished! Elapsed time: 100s

jcohenadad · February 26, 2020, 4:39pm

I found another error when trying to erode an image:
rosella@vivi:~/spinal_cord/1$ sct_maths -i kurtosis_crop_moco_dwi_mean.nii -erode 3,3,3 -o thr_seg.nii

Morphological mathematic operation (e.g., dilation, erosion) should only be applied to binary data. Here you applied it to a grayscale data.

jcohenadad · February 26, 2020, 4:50pm

Regarding this error:

   AttributeError: module 'tensorflow_core._api.v2.config' has no attribute 'experimental_list_devices'

This is likely due to a recent deprecation in tensorflow. Given that you updated you OS recently, and that you were able to run tensorflow + scipy + pyQT functions in your recent installations, maybe you could try to re-install the latest version (4.2.1) and try running sct_testing -d 1 again. Would you mind trying that? Sorry for all these issues…

Rosella_Tro · February 26, 2020, 4:50pm

Is _seg.nii image produced by segmentation a binary image?
THanks
ROsella

jcohenadad · February 26, 2020, 5:23pm

Is _seg.nii image produced by segmentation a binary image?

yes

Rosella_Tro · February 27, 2020, 1:28pm

Hi.
I can’t understand why it gives the same error also trying to erode the segmented mask

sct_maths -erode 3,3,3 -i kurtosis_crop_moco_dwi_mean_seg.nii -o thresh_seg.nii

--
Spinal Cord Toolbox (4.1.0)

Traceback (most recent call last):
  File "/home/rosella/sct_4.1.0/scripts/sct_maths.py", line 774, in <module>
    main()
  File "/home/rosella/sct_4.1.0/scripts/sct_maths.py", line 342, in main
    data_out = erode(data, convert_list_str(arguments.erode))
TypeError: convert_list_str() missing 1 required positional argument: 'type'

jcohenadad · February 27, 2020, 2:02pm

hum, that’s strange. Could you upload your file kurtosis_crop_moco_dwi_mean_seg.nii ?

Rosella_Tro · February 27, 2020, 2:05pm

kurtosis_crop_moco_dwi_mean_seg.nii (6.9 KB)
Here is the image,
thanks,
Rosella

jcohenadad · February 27, 2020, 3:58pm

Hi Rosella,
I am able to reproduce your error. This is a bug. A ticket has been opened here and we will fix it with high priority.
Thank you for reporting it!
Julien

jcohenadad · February 27, 2020, 8:22pm

The issue has now been fixed on the master branch. It will be available in SCT 4.2.2. release.