Error installing SCT 4.2.2

Hi,

I am trying to install SCT 4.2.2 on my university HPC but I get an error which I have pasted below.

I am using the following Linux distribution:
Static hostname: m3-login3
Icon name: computer-vm
Chassis: vm
Machine ID: ed407a0d5d79421bb1fd5040b847d039
Boot ID: 89395468b0124930b634a4fbbc64905d
Virtualization: kvm
Operating System: CentOS Linux 7 (Core)
CPE OS Name: cpe:/o:centos:centos:7
Kernel: Linux 3.10.0-1127.18.2.el7.x86_64
Architecture: x86-64

I appreciate any help with this. Thank you!

Cheers,

Will

./install_sct


  • Welcome to SCT installation *

Checking OS type and version…

Linux m3p006 3.10.0-1127.18.2.el7.x86_64 #1 SMP Sun Jul 26 15:27:06 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Checking requirements…

OK!

SCT version … 4.2.2
Installation type … package
Operating system … linux (unknown)
Shell config … /home/willk/.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/willk/sct_4.2.2]

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

Choose install directory. Warning! Give full path (e.g. /usr/django/sct_v3.0):
/home/willk/fj32_scratch/will/sct_4.2.2

Copying source files from /home/willk/Downloads/spinalcordtoolbox-4.2.2 to /home/willk/fj32_scratch/will/sct_4.2.2


Installing conda…

rm -rf /home/willk/fj32_scratch/will/sct_4.2.2/python

mkdir -p /home/willk/fj32_scratch/will/sct_4.2.2/python

wget -O /tmp/tmp.98v2RlJ1hz/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

–2020-09-29 13:30:41-- https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
wget: /home/willk/.netrc:2: unknown token “user”
wget: /home/willk/.netrc:2: unknown token “d258ab0d-f3d9-4bb3-9129-6a42f7dc014c”
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… 301 Moved Permanently
Location: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [following]
–2020-09-29 13:30:42-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.anaconda.com (repo.anaconda.com)… 104.16.130.3, 104.16.131.3, 2606:4700::6810:8203, …
Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.130.3|:443… connected.
HTTP request sent, awaiting response… 200 OK
Length: 93052469 (89M) [application/x-sh]
Saving to: \u2018/tmp/tmp.98v2RlJ1hz/miniconda.sh\u2019

100%[=====================================================================================================================================>] 93,052,469 101MB/s in 0.9s

2020-09-29 13:30:43 (101 MB/s) - \u2018/tmp/tmp.98v2RlJ1hz/miniconda.sh\u2019 saved [93052469/93052469]

exit status is 0

bash /tmp/tmp.98v2RlJ1hz/miniconda.sh -p /home/willk/fj32_scratch/will/sct_4.2.2/python -b -f

PREFIX=/home/willk/fj32_scratch/will/sct_4.2.2/python
Unpacking payload …
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /home/willk/fj32_scratch/will/sct_4.2.2/python

added / updated specs:
- _libgcc_mutex==0.1=main
- ca-certificates==2020.1.1=0
- certifi==2020.4.5.1=py38_0
- cffi==1.14.0=py38he30daa8_1
- chardet==3.0.4=py38_1003
- conda-package-handling==1.6.1=py38h7b6447c_0
- conda==4.8.3=py38_0
- cryptography==2.9.2=py38h1ba5d50_0
- idna==2.9=py_1
- ld_impl_linux-64==2.33.1=h53a641e_7
- libedit==3.1.20181209=hc058e9b_0
- libffi==3.3=he6710b0_1
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- ncurses==6.2=he6710b0_1
- openssl==1.1.1g=h7b6447c_0
- pip==20.0.2=py38_3
- pycosat==0.6.3=py38h7b6447c_1
- pycparser==2.20=py_0
- pyopenssl==19.1.0=py38_0
- pysocks==1.7.1=py38_0
- python==3.8.3=hcff3b4d_0
- readline==8.0=h7b6447c_0
- requests==2.23.0=py38_0
- ruamel_yaml==0.15.87=py38h7b6447c_0
- setuptools==46.4.0=py38_0
- six==1.14.0=py38_0
- sqlite==3.31.1=h62c20be_1
- tk==8.6.8=hbc83047_0
- tqdm==4.46.0=py_0
- urllib3==1.25.8=py38_0
- wheel==0.34.2=py38_0
- xz==5.2.5=h7b6447c_0
- 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
ca-certificates pkgs/main/linux-64::ca-certificates-2020.1.1-0
certifi pkgs/main/linux-64::certifi-2020.4.5.1-py38_0
cffi pkgs/main/linux-64::cffi-1.14.0-py38he30daa8_1
chardet pkgs/main/linux-64::chardet-3.0.4-py38_1003
conda pkgs/main/linux-64::conda-4.8.3-py38_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.1-py38h7b6447c_0
cryptography pkgs/main/linux-64::cryptography-2.9.2-py38h1ba5d50_0
idna pkgs/main/noarch::idna-2.9-py_1
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-3.3-he6710b0_1
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_1
openssl pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
pip pkgs/main/linux-64::pip-20.0.2-py38_3
pycosat pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
pycparser pkgs/main/noarch::pycparser-2.20-py_0
pyopenssl pkgs/main/linux-64::pyopenssl-19.1.0-py38_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py38_0
python pkgs/main/linux-64::python-3.8.3-hcff3b4d_0
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
requests pkgs/main/linux-64::requests-2.23.0-py38_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py38h7b6447c_0
setuptools pkgs/main/linux-64::setuptools-46.4.0-py38_0
six pkgs/main/linux-64::six-1.14.0-py38_0
sqlite pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
tk pkgs/main/linux-64::tk-8.6.8-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.46.0-py_0
urllib3 pkgs/main/linux-64::urllib3-1.25.8-py38_0
wheel pkgs/main/linux-64::wheel-0.34.2-py38_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
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: 4.8.3
latest version: 4.8.5

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /home/willk/fj32_scratch/will/sct_4.2.2/python/envs/venv_sct

added / updated specs:
- python=3.6

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
ca-certificates-2020.7.22  |                0         125 KB
certifi-2020.6.20          |           py36_0         156 KB
libedit-3.1.20191231       |       h14c3975_1         116 KB
libffi-3.3                 |       he6710b0_2          50 KB
openssl-1.1.1h             |       h7b6447c_0         2.5 MB
pip-20.2.2                 |           py36_0         1.8 MB
python-3.6.12              |       hcff3b4d_2        29.7 MB
setuptools-49.6.0          |           py36_1         728 KB
sqlite-3.33.0              |       h62c20be_0         1.1 MB
tk-8.6.10                  |       hbc83047_0         3.0 MB
wheel-0.35.1               |             py_0          37 KB
------------------------------------------------------------
                                       Total:        39.3 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-2020.7.22-0
certifi pkgs/main/linux-64::certifi-2020.6.20-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-3.1.20191231-h14c3975_1
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
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_1
openssl pkgs/main/linux-64::openssl-1.1.1h-h7b6447c_0
pip pkgs/main/linux-64::pip-20.2.2-py36_0
python pkgs/main/linux-64::python-3.6.12-hcff3b4d_2
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
setuptools pkgs/main/linux-64::setuptools-49.6.0-py36_1
sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0
tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0
wheel pkgs/main/noarch::wheel-0.35.1-py_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Proceed ([y]/n)?

Downloading and Extracting Packages
setuptools-49.6.0 | 728 KB | #################################################################################################################################### | 100%
certifi-2020.6.20 | 156 KB | #################################################################################################################################### | 100%
python-3.6.12 | 29.7 MB | #################################################################################################################################### | 100%
pip-20.2.2 | 1.8 MB | #################################################################################################################################### | 100%
libedit-3.1.20191231 | 116 KB | #################################################################################################################################### | 100%
wheel-0.35.1 | 37 KB | #################################################################################################################################### | 100%
ca-certificates-2020 | 125 KB | #################################################################################################################################### | 100%
sqlite-3.33.0 | 1.1 MB | #################################################################################################################################### | 100%
openssl-1.1.1h | 2.5 MB | #################################################################################################################################### | 100%
tk-8.6.10 | 3.0 MB | #################################################################################################################################### | 100%
libffi-3.3 | 50 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-1.19.2-cp36-cp36m-manylinux2010_x86_64.whl (14.5 MB)
Installing collected packages: numpy
Successfully installed numpy-1.19.2

Using requirements-freeze.txt (release installation)

Processing /home/willk/.cache/pip/wheels/c3/af/84/3962a6af7b4ab336e951b7877dcfb758cf94548bb1771e0679/absl_py-0.9.0-py3-none-any.whl
Collecting astor==0.8.1
Using cached astor-0.8.1-py2.py3-none-any.whl (27 kB)
Collecting attrs==19.3.0
Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Collecting cachetools==4.0.0
Using cached cachetools-4.0.0-py3-none-any.whl (10 kB)
Collecting certifi==2019.11.28
Using cached certifi-2019.11.28-py2.py3-none-any.whl (156 kB)
Collecting cffi==1.13.2
Using cached cffi-1.13.2-cp36-cp36m-manylinux1_x86_64.whl (397 kB)
Collecting chardet==3.0.4
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting coverage==5.0
Using cached coverage-5.0-cp36-cp36m-manylinux1_x86_64.whl (226 kB)
Collecting cryptography==2.8
Using cached cryptography-2.8-cp34-abi3-manylinux2010_x86_64.whl (2.3 MB)
Collecting cycler==0.10.0
Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting decorator==4.4.1
Using cached decorator-4.4.1-py2.py3-none-any.whl (9.2 kB)
Collecting dipy==1.0.0
Using cached dipy-1.0.0-cp36-cp36m-manylinux1_x86_64.whl (8.1 MB)
Collecting futures==3.1.1
Using cached futures-3.1.1-py3-none-any.whl (2.8 kB)
Processing /home/willk/.cache/pip/wheels/19/a7/b9/0740c7a3a7d1d348f04823339274b90de25fbcd217b2ee1fbe/gast-0.2.2-py3-none-any.whl
Collecting google-auth==1.10.0
Using cached google_auth-1.10.0-py2.py3-none-any.whl (76 kB)
Collecting google-auth-oauthlib==0.4.1
Using cached google_auth_oauthlib-0.4.1-py2.py3-none-any.whl (18 kB)
Collecting google-pasta==0.1.8
Using cached google_pasta-0.1.8-py3-none-any.whl (57 kB)
Collecting grpcio==1.26.0
Using cached grpcio-1.26.0-cp36-cp36m-manylinux2010_x86_64.whl (2.4 MB)
Collecting h5py==2.10.0
Using cached h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB)
Collecting idna==2.8
Using cached idna-2.8-py2.py3-none-any.whl (58 kB)
Collecting imageio==2.6.1
Using cached imageio-2.6.1-py3-none-any.whl (3.3 MB)
Collecting importlib-metadata==1.3.0
Using cached importlib_metadata-1.3.0-py2.py3-none-any.whl (29 kB)
Collecting joblib==0.14.1
Using cached joblib-0.14.1-py2.py3-none-any.whl (294 kB)
Collecting Keras==2.3.1
Using cached Keras-2.3.1-py2.py3-none-any.whl (377 kB)
Collecting Keras-Applications==1.0.8
Using cached Keras_Applications-1.0.8-py3-none-any.whl (50 kB)
Collecting Keras-Preprocessing==1.1.0
Using cached Keras_Preprocessing-1.1.0-py2.py3-none-any.whl (41 kB)
Collecting kiwisolver==1.1.0
Using cached kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90 kB)
Collecting Markdown==3.1.1
Using cached Markdown-3.1.1-py2.py3-none-any.whl (87 kB)
Collecting matplotlib==3.1.2
Using cached matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl (13.1 MB)
Collecting more-itertools==8.0.2
Using cached more_itertools-8.0.2-py3-none-any.whl (40 kB)
Collecting networkx==2.4
Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
Collecting nibabel==3.0.0
Using cached nibabel-3.0.0-py3-none-any.whl (3.3 MB)
Collecting numpy==1.17.4
Using cached numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl (20.0 MB)
Collecting oauthlib==3.1.0
Using cached oauthlib-3.1.0-py2.py3-none-any.whl (147 kB)
Processing /home/willk/.cache/pip/wheels/1f/6f/14/e0f4f6bceec756bbab45c392c4d5429a684b14d849464ebfbf/opt_einsum-3.1.0-py3-none-any.whl
Collecting packaging==19.2
Using cached packaging-19.2-py2.py3-none-any.whl (30 kB)
Collecting pandas==0.25.3
Using cached pandas-0.25.3-cp36-cp36m-manylinux1_x86_64.whl (10.4 MB)
Collecting Pillow==6.2.1
Using cached Pillow-6.2.1-cp36-cp36m-manylinux1_x86_64.whl (2.1 MB)
Collecting pluggy==0.13.1
Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting protobuf==3.11.1
Using cached protobuf-3.11.1-cp36-cp36m-manylinux1_x86_64.whl (1.3 MB)
Processing /home/willk/.cache/pip/wheels/b2/b3/a3/551db06cebc9141c437c6b58aa751d3670471494e9f6d1428d/psutil-5.6.7-cp36-cp36m-linux_x86_64.whl
Collecting py==1.8.0
Using cached py-1.8.0-py2.py3-none-any.whl (83 kB)
Collecting pyasn1==0.4.8
Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting pyasn1-modules==0.2.7
Using cached pyasn1_modules-0.2.7-py2.py3-none-any.whl (131 kB)
Processing /home/willk/.cache/pip/wheels/c6/6b/83/2608afaa57ecfb0a66ac89191a8d9bad71c62ca55ee499c2d0/pycparser-2.19-py2.py3-none-any.whl
Collecting pyOpenSSL==19.1.0
Using cached pyOpenSSL-19.1.0-py2.py3-none-any.whl (53 kB)
Collecting pyparsing==2.4.5
Using cached pyparsing-2.4.5-py2.py3-none-any.whl (67 kB)
Collecting PyQt5==5.11.3
Using cached PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8 MB)
Collecting PyQt5-sip==4.19.19
Using cached PyQt5_sip-4.19.19-cp36-cp36m-manylinux1_x86_64.whl (67 kB)
Collecting pytest==5.3.2
Using cached pytest-5.3.2-py3-none-any.whl (234 kB)
Collecting pytest-cov==2.8.1
Using cached pytest_cov-2.8.1-py2.py3-none-any.whl (18 kB)
Collecting python-dateutil==2.8.1
Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pytz==2019.3
Using cached pytz-2019.3-py2.py3-none-any.whl (509 kB)
Collecting PyWavelets==1.1.1
Using cached PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (4.4 MB)
Processing /home/willk/.cache/pip/wheels/af/4b/a6/d492db4435642aebd1df1cd3ed075815e75ad6665aa47f4d04/PyYAML-5.2-cp36-cp36m-linux_x86_64.whl
Collecting raven==6.10.0
Using cached raven-6.10.0-py2.py3-none-any.whl (284 kB)
Collecting requests==2.22.0
Using cached requests-2.22.0-py2.py3-none-any.whl (57 kB)
Collecting requests-oauthlib==1.3.0
Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB)
Collecting rsa==4.0
Using cached rsa-4.0-py2.py3-none-any.whl (38 kB)
Collecting scikit-image==0.16.2
Using cached scikit_image-0.16.2-cp36-cp36m-manylinux1_x86_64.whl (26.5 MB)
Collecting scikit-learn==0.22
Using cached scikit_learn-0.22-cp36-cp36m-manylinux1_x86_64.whl (7.0 MB)
Collecting scipy==1.4.0
Using cached scipy-1.4.0-cp36-cp36m-manylinux1_x86_64.whl (26.1 MB)
Collecting six==1.13.0
Using cached six-1.13.0-py2.py3-none-any.whl (10 kB)
Collecting tensorboard==2.0.2
Using cached tensorboard-2.0.2-py3-none-any.whl (3.8 MB)
Collecting tensorflow==2.0.1
Using cached tensorflow-2.0.1-cp36-cp36m-manylinux2010_x86_64.whl (86.3 MB)
Collecting tensorflow-estimator==2.0.1
Using cached tensorflow_estimator-2.0.1-py2.py3-none-any.whl (449 kB)
Processing /home/willk/.cache/pip/wheels/93/2a/eb/e58dbcbc963549ee4f065ff80a59f274cc7210b6eab962acdc/termcolor-1.1.0-py3-none-any.whl
Collecting tqdm==4.40.2
Using cached tqdm-4.40.2-py2.py3-none-any.whl (55 kB)
Processing /home/willk/.cache/pip/wheels/be/7a/eb/465e9bb085af816c4d504821d542cc0059cc3433f6e8edea3c/transforms3d-0.3.1-py3-none-any.whl
Collecting urllib3==1.25.7
Using cached urllib3-1.25.7-py2.py3-none-any.whl (125 kB)
Collecting wcwidth==0.1.7
Using cached wcwidth-0.1.7-py2.py3-none-any.whl (21 kB)
Collecting Werkzeug==0.16.0
Using cached Werkzeug-0.16.0-py2.py3-none-any.whl (327 kB)
Processing /home/willk/.cache/pip/wheels/0d/85/48/15d7bfab92a2d0e87372224c1f628fc57db7447a663a58e86c/wrapt-1.11.2-cp36-cp36m-linux_x86_64.whl
Collecting xlrd==1.2.0
Using cached xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
Collecting xlutils==2.0.0
Using cached xlutils-2.0.0-py2.py3-none-any.whl (55 kB)
Collecting xlwt==1.3.0
Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
Collecting zipp==0.6.0
Using cached zipp-0.6.0-py2.py3-none-any.whl (4.1 kB)
Requirement already satisfied: setuptools>=40.3.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth==1.10.0->-r requirements-freeze.txt (line 15)) (49.6.0.post20200925)
Requirement already satisfied: wheel>=0.26; python_version >= “3” in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard==2.0.2->-r requirements-freeze.txt (line 64)) (0.35.1)
Installing collected packages: six, absl-py, astor, attrs, cachetools, certifi, pycparser, cffi, chardet, coverage, cryptography, cycler, decorator, numpy, scipy, h5py, nibabel, dipy, futures, gast, pyasn1, rsa, pyasn1-modules, google-auth, oauthlib, idna, urllib3, requests, requests-oauthlib, google-auth-oauthlib, google-pasta, grpcio, Pillow, imageio, more-itertools, zipp, importlib-metadata, joblib, PyYAML, Keras-Preprocessing, Keras-Applications, Keras, kiwisolver, Markdown, pyparsing, python-dateutil, matplotlib, networkx, opt-einsum, packaging, pytz, pandas, pluggy, protobuf, psutil, py, pyOpenSSL, PyQt5-sip, PyQt5, wcwidth, pytest, pytest-cov, PyWavelets, raven, scikit-image, scikit-learn, Werkzeug, tensorboard, wrapt, termcolor, tensorflow-estimator, tensorflow, tqdm, transforms3d, xlrd, xlwt, xlutils
Attempting uninstall: certifi
Found existing installation: certifi 2020.6.20
Uninstalling certifi-2020.6.20:
Successfully uninstalled certifi-2020.6.20
Attempting uninstall: numpy
Found existing installation: numpy 1.19.2
Uninstalling numpy-1.19.2:
Successfully uninstalled numpy-1.19.2
Successfully installed Keras-2.3.1 Keras-Applications-1.0.8 Keras-Preprocessing-1.1.0 Markdown-3.1.1 Pillow-6.2.1 PyQt5-5.11.3 PyQt5-sip-4.19.19 PyWavelets-1.1.1 PyYAML-5.2 Werkzeug-0.16.0 absl-py-0.9.0 astor-0.8.1 attrs-19.3.0 cachetools-4.0.0 certifi-2019.11.28 cffi-1.13.2 chardet-3.0.4 coverage-5.0 cryptography-2.8 cycler-0.10.0 decorator-4.4.1 dipy-1.0.0 futures-3.1.1 gast-0.2.2 google-auth-1.10.0 google-auth-oauthlib-0.4.1 google-pasta-0.1.8 grpcio-1.26.0 h5py-2.10.0 idna-2.8 imageio-2.6.1 importlib-metadata-1.3.0 joblib-0.14.1 kiwisolver-1.1.0 matplotlib-3.1.2 more-itertools-8.0.2 networkx-2.4 nibabel-3.0.0 numpy-1.17.4 oauthlib-3.1.0 opt-einsum-3.1.0 packaging-19.2 pandas-0.25.3 pluggy-0.13.1 protobuf-3.11.1 psutil-5.6.7 py-1.8.0 pyOpenSSL-19.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.7 pycparser-2.19 pyparsing-2.4.5 pytest-5.3.2 pytest-cov-2.8.1 python-dateutil-2.8.1 pytz-2019.3 raven-6.10.0 requests-2.22.0 requests-oauthlib-1.3.0 rsa-4.0 scikit-image-0.16.2 scikit-learn-0.22 scipy-1.4.0 six-1.13.0 tensorboard-2.0.2 tensorflow-2.0.1 tensorflow-estimator-2.0.1 termcolor-1.1.0 tqdm-4.40.2 transforms3d-0.3.1 urllib3-1.25.7 wcwidth-0.1.7 wrapt-1.11.2 xlrd-1.2.0 xlutils-2.0.0 xlwt-1.3.0 zipp-0.6.0
Obtaining file:///home/willk/fj32_scratch/will/sct_4.2.2
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/willk/fj32_scratch/will/sct_4.2.2/bin


Spinal Cord Toolbox (4.2.2)

Folder /home/willk/fj32_scratch/will/sct_4.2.2/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 [00:05<00:00, 15.5MB/s]

Create temporary folder (/tmp/sct-20200929133248.726552-dr3dhal2)…

Unzip data to: /tmp/sct-20200929133248.726552-dr3dhal2

Check if folder already exists on the destination path…

Remove temporary folders…
Done!

All requirements installed!

. /home/willk/fj32_scratch/will/sct_4.2.2/python/bin/activate /home/willk/fj32_scratch/will/sct_4.2.2/python

Installing data…

rm -rf /home/willk/fj32_scratch/will/sct_4.2.2/data

mkdir -p /home/willk/fj32_scratch/will/sct_4.2.2/data

cd /home/willk/fj32_scratch/will/sct_4.2.2/data

sct_download_data -d PAM50


Spinal Cord Toolbox (4.2.2)

Trying URL: https://osf.io/u79sr/?pid=6zbyf/?action=download
Unexpected: link doesn’t provide a filename

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20191029_PAM50.zip
Unexpected: link doesn’t provide a filename

Download error

Create temporary folder (/tmp/sct-20200929133253.677857-elq2q4ce)…

Unzip data to: /tmp/sct-20200929133253.677857-elq2q4ce
Traceback (most recent call last):
File “/fs03/fj32/will/sct_4.2.2/scripts/sct_download_data.py”, line 248, in
res = main()
File “/fs03/fj32/will/sct_4.2.2/scripts/sct_download_data.py”, line 140, in main
unzip(tmp_file, dest_tmp_folder, verbose)
File “/fs03/fj32/will/sct_4.2.2/scripts/sct_download_data.py”, line 174, in unzip
if compressed.endswith(‘zip’):
AttributeError: ‘NoneType’ object has no attribute ‘endswith’

Hi, Will! I’m sorry to hear you’re having trouble.

The newest version of SCT is Version 4.3. Could you try installing this version? (Version 4.3 includes some changes that I believe address this issue.)

Hi Joshua,

Thanks for this. Under normal circumstances, I would have installed the latest version but we actually have a specific pipeline that we are trying to use with 4.2.2. Is there any way around this?

I have also tried installing this locally on my Mac (OS Catalina 10.15.7) and realised that the dialog box doesn’t work when running the following command - Do you think this might have something to do with the zsh shell?

sct_label_utils -i subject_t1.nii.gz -create-viewer 3,4 -o subject_t1_labels_disc.nii.gz -msg “Place label at the posterior tip of each inter-vertebral disc. E.g. label 3: C2/C3.”

Cheers!

Will

Hi Will,

Thank you so much for providing that extra context. :slight_smile:


The fix for the first error was included in v4.3, but it was a relatively small change to SCT’s code. (If you’re curious, it is this GitHub commit.)

So, one option we have for fixing the issue while preserving 4.2.2 behavior would be to manually apply only this change. Doing this is admittedly a bit hacky, but given the circumstances, it might be the best option. I’ve tried this out on my own machine and it fixed the issue.

Could you try replacing the file spinalcordtoolbox-4.2.2/scripts/sct_download_data.py with this modified file that includes the fix: sct_download_data.py (9.9 KB)? Then, try rerunning install_sct.


Also, just out of curiosity, could you share more about why your pipeline requires 4.2.2 specifically? Just to help us better understand the contexts that SCT is being used in. :slightly_smiling_face: