Unable to install sct due to tensorflow fail


#1

Hello! I ran into some errors while installing sct. Looks like tensorflow could not be installed. Any idea how I can install that? I am running a macOS El Capitan version 10.11.6 on a mid-2007 iMac. Here is the last section of the message during installation. Thanks.

Validate installation...
SCT info:
- version: 4.0.0-beta.5
- path: /Users/shazeebm/sct_4.0.0-beta.5
OS: osx (Darwin-15.6.0-x86_64-i386-64bit)
CPU cores: Available: 2, Used by SCT: 2
RAM: Primary memory available: 4.00 gigabytes
Check Python executable.............................[OK]
  Using bundled python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] at /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.16.4)
Check if cryptography is installed..................[OK] (2.7)
Check if dipy is installed..........................[OK] (0.16.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.9.0)
Check if Keras is installed.........................[FAIL]
Check if matplotlib is installed....................[OK] (3.1.0)
Check if nibabel is installed.......................[OK] (2.4.1)
Check if pandas is installed........................[OK] (0.24.2)
Check if psutil is installed........................[OK] (5.6.2)
Check if pyqt5 is installed.........................[OK]
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.22.0)
Check if scipy is installed.........................[OK] (1.3.0)
Check if scikit-image is installed..................Could not open font file /System/Library/Fonts/Apple Color Emoji.ttf: In FT2Font: Could not set the fontsize
Could not open font file /Library/Fonts/NISC18030.ttf: In FT2Font: Could not set the fontsize
generated new fontManager
[OK] (0.15.0)
Check if scikit-learn is installed..................[OK] (0.21.2)
Check if tensorflow is installed....................[FAIL]
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] (4.32.1)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.3)
Check if git+https://github.com/jcohenadad/nipy.git is installed[OK] (0.5.0.dev)
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]

Installation validation Failed!
Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):
http://forum.spinalcordmri.org/c/sct

Installation failed

#2

Hi,

Unfortunately, with the recent move to Python 3.x we had to upgrade the version of TensorFlow and consequently lost compatibility with OSX below Sierra (<10.12).

Could you upgrade to High Sierra (or Mojave) on your Mac? If not, could you use SCT via Docker as explained here?

If this is too much trouble for you, let me know and we will try to find a solution to ensure compatibility with OSX 10.11.

Cheers,
Julien


#3

Thank you so much for your prompt response. Unfortunately, this system cannot be upgraded beyond El Capitan 10.11.6. I will try the Docker and see if that works and let you know. Thanks again!

-Salman-


#4

Dear Julien,

It turns out that I can’t install Docker since my iMac hardware is mid-2007 and Docker requires at least 2010. Do you have any other suggestions as to how I could run SCT on this archaic machine? Again, this is a mid-2007 iMac with 10.11.6 El Capitan, 4GB 667 MHz DDR2 SDRAM, 2.4 GHz Intel Core 2 Duo, ATI Radeon HD 2600 Pro 256 MB. Let me know if you need more info.

Thanks for you help!

Best Regards,

-Salman-


#5

Hi Salman,
We will try to work on a solution. Ticket opened here.
Best,
Julien


#6

Hi Salman,

We fixed the compatibility issue with El Capitan. Before we make a release, would you be able to test the installation with git? Try to run:

git clone --branch=master https://github.com/neuropoly/spinalcordtoolbox.git sct
cd sct
./install_sct

Let us know how it goes,
Best,
Julien


#7

Hi Julien,

Thanks so much for looking into this. I did run it and ran into some error with the Keras installation part. I am pasting the last part of the output below. Thanks again.

Validate installation...

--

Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)

SCT info:

- version: git-master-567a67e2508704061e348d20b54cbb7963f20daa

- path: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct

OS: osx (Darwin-15.6.0-x86_64-i386-64bit)

CPU cores: Available: 2, Used by SCT: 2

RAM: Primary memory available: 4.00 gigabytes

Check Python executable.............................[OK]

Using bundled python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46) 

[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] at /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/python/envs/venv_sct/bin/python

Check if data are installed.........................[OK]

Check if numpy is installed.........................[OK] (1.16.4)

Check if cryptography is installed..................[OK] (2.7)

Check if dipy is installed..........................[OK] (0.16.0)

Check if futures is installed.......................[OK]

Check if h5py is installed..........................[OK] (2.9.0)

Check if Keras is installed........................../install_sct: line 576: 34946 Illegal instruction: 4 sct_check_dependencies

Installation validation Failed!

Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):

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

Installation failed

#8

Hi
Could you please paste the entire installation output so I can check what went wrong? You can use pastebin.com for large copy/paste


#9

Sure. Here it is:

ipac-imac:spinalcordtoolbox-4.0.0-beta.5 shazeebm$ git clone --branch=master https://github.com/neuropoly/spinalcordtoolbox.git sct
Cloning into 'sct'...
remote: Enumerating objects: 213, done.
remote: Counting objects: 100% (213/213), done.
remote: Compressing objects: 100% (134/134), done.
remote: Total 43145 (delta 124), reused 135 (delta 79), pack-reused 42932
Receiving objects: 100% (43145/43145), 156.17 MiB | 8.55 MiB/s, done.
Resolving deltas: 100% (28212/28212), done.
ipac-imac:spinalcordtoolbox-4.0.0-beta.5 shazeebm$ cd sct
ipac-imac:sct shazeebm$ ./install_sct

Welcome to the SCT installer!

SCT version ......... dev
Installation type ... in-place
Operating system .... osx
Shell ............... /Users/shazeebm/.bashrc
sudo mode ........... 0

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: [/Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct]
Do you agree? [y]es/[n]o: y

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

Installing conda...
>> rm -rf /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/python
>> mkdir -p /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/python
>> curl -o /var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/tmp.BAMnHHOd/miniconda.sh -L https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 44.0M  100 44.0M    0     0  4535k      0  0:00:09  0:00:09 --:--:-- 5374k
exit status is 0
>> bash /var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/tmp.BAMnHHOd/miniconda.sh -p /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/python -b -f
PREFIX=/Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/python
reinstalling: python-3.7.3-h359304d_0 ...
using -f (force) option
Python 3.7.3
reinstalling: ca-certificates-2019.1.23-0 ...
using -f (force) option
reinstalling: libcxxabi-4.0.1-hcfea43d_1 ...
using -f (force) option
reinstalling: xz-5.2.4-h1de35cc_4 ...
using -f (force) option
reinstalling: yaml-0.1.7-hc338f04_2 ...
using -f (force) option
reinstalling: zlib-1.2.11-h1de35cc_3 ...
using -f (force) option
reinstalling: libcxx-4.0.1-hcfea43d_1 ...
using -f (force) option
reinstalling: openssl-1.1.1b-h1de35cc_1 ...
using -f (force) option
reinstalling: tk-8.6.8-ha441bb4_0 ...
using -f (force) option
reinstalling: libffi-3.2.1-h475c297_4 ...
using -f (force) option
reinstalling: ncurses-6.1-h0a44026_1 ...
using -f (force) option
reinstalling: libedit-3.1.20181209-hb402a30_0 ...
using -f (force) option
reinstalling: readline-7.0-h1de35cc_5 ...
using -f (force) option
reinstalling: sqlite-3.27.2-ha441bb4_0 ...
using -f (force) option
reinstalling: asn1crypto-0.24.0-py37_0 ...
using -f (force) option
reinstalling: certifi-2019.3.9-py37_0 ...
using -f (force) option
reinstalling: chardet-3.0.4-py37_1 ...
using -f (force) option
reinstalling: idna-2.8-py37_0 ...
using -f (force) option
reinstalling: pycosat-0.6.3-py37h1de35cc_0 ...
using -f (force) option
reinstalling: pycparser-2.19-py37_0 ...
using -f (force) option
reinstalling: pysocks-1.6.8-py37_0 ...
using -f (force) option
reinstalling: python.app-2-py37_9 ...
using -f (force) option
reinstalling: ruamel_yaml-0.15.46-py37h1de35cc_0 ...
using -f (force) option
reinstalling: six-1.12.0-py37_0 ...
using -f (force) option
reinstalling: cffi-1.12.2-py37hb5b8e2f_1 ...
using -f (force) option
reinstalling: setuptools-41.0.0-py37_0 ...
using -f (force) option
reinstalling: cryptography-2.6.1-py37ha12b0ac_0 ...
using -f (force) option
reinstalling: wheel-0.33.1-py37_0 ...
using -f (force) option
reinstalling: pip-19.0.3-py37_0 ...
using -f (force) option
reinstalling: pyopenssl-19.0.0-py37_0 ...
using -f (force) option
reinstalling: urllib3-1.24.1-py37_0 ...
using -f (force) option
reinstalling: requests-2.21.0-py37_0 ...
using -f (force) option
reinstalling: conda-4.6.14-py37_0 ...
using -f (force) option
using -f (force) option
installation finished.
Conda installation successful
Collecting package metadata: done
Solving environment: done

## Package Plan ##

  environment location: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/python/envs/venv_sct

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2019.5.15  |                0         133 KB
    certifi-2019.3.9           |           py36_0         155 KB
    openssl-1.1.1c             |       h1de35cc_1         3.4 MB
    pip-19.1.1                 |           py36_0         1.9 MB
    python-3.6.8               |       haf84260_0        20.5 MB
    setuptools-41.0.1          |           py36_0         641 KB
    sqlite-3.28.0              |       ha441bb4_0         2.3 MB
    wheel-0.33.4               |           py36_0          39 KB
    ------------------------------------------------------------
                                           Total:        29.1 MB

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2019.5.15-0
  certifi            pkgs/main/osx-64::certifi-2019.3.9-py36_0
  libcxx             pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
  libcxxabi          pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.2.1-h475c297_4
  ncurses            pkgs/main/osx-64::ncurses-6.1-h0a44026_1
  openssl            pkgs/main/osx-64::openssl-1.1.1c-h1de35cc_1
  pip                pkgs/main/osx-64::pip-19.1.1-py36_0
  python             pkgs/main/osx-64::python-3.6.8-haf84260_0
  readline           pkgs/main/osx-64::readline-7.0-h1de35cc_5
  setuptools         pkgs/main/osx-64::setuptools-41.0.1-py36_0
  sqlite             pkgs/main/osx-64::sqlite-3.28.0-ha441bb4_0
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  wheel              pkgs/main/osx-64::wheel-0.33.4-py36_0
  xz                 pkgs/main/osx-64::xz-5.2.4-h1de35cc_4
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Proceed ([y]/n)? 

Downloading and Extracting Packages
wheel-0.33.4         | 39 KB     | ##################################################################################################### | 100% 
python-3.6.8         | 20.5 MB   | ##################################################################################################### | 100% 
openssl-1.1.1c       | 3.4 MB    | ##################################################################################################### | 100% 
certifi-2019.3.9     | 155 KB    | ##################################################################################################### | 100% 
ca-certificates-2019 | 133 KB    | ##################################################################################################### | 100% 
setuptools-41.0.1    | 641 KB    | ##################################################################################################### | 100% 
sqlite-3.28.0        | 2.3 MB    | ##################################################################################################### | 100% 
pip-19.1.1           | 1.9 MB    | ##################################################################################################### | 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 https://files.pythonhosted.org/packages/0f/c9/3526a357b6c35e5529158fbcfac1bb3adc8827e8809a6d254019d326d1cc/numpy-1.16.4-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Installing collected packages: numpy
Successfully installed numpy-1.16.4
Ignoring tensorflow: markers 'platform_system != "Darwin" or "15." not 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)) (1.16.4)
Collecting cryptography (from -r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/63/4e/57b7a6bd98906872fcd2531e74b532de2abe17d675a5cf171931fcb4a9e8/cryptography-2.7-cp34-abi3-macosx_10_6_intel.whl
Collecting dipy (from -r requirements.txt (line 3))
  Using cached https://files.pythonhosted.org/packages/62/8f/63fe5e03244b0044307bcb9742df367ebcd6b00220c7ce1d16150fd5bcdb/dipy-0.16.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting futures (from -r requirements.txt (line 4))
Collecting h5py (from -r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/03/21/1cdf7fa7868528b35c1a08a770eb9334279574a8b5f1d7a2966dcec14e42/h5py-2.9.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting Keras (from -r requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/5e/10/aa32dad071ce52b5502266b5c659451cfd6ffcbf14e6c8c4f16c0ff5aaab/Keras-2.2.4-py2.py3-none-any.whl
Collecting matplotlib (from -r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/45/bf/8d8233749b5f8580bdfdb2aeed0d2df177daab44cfebc5c0de827ce1b11e/matplotlib-3.1.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting nibabel (from -r requirements.txt (line 8))
  Using cached https://files.pythonhosted.org/packages/66/30/fbed62172920c3fd050b6483541546a87c5e735f4a0ef03f08bb150680b4/nibabel-2.4.1-py2.py3-none-any.whl
Collecting pandas (from -r requirements.txt (line 9))
  Using cached https://files.pythonhosted.org/packages/2a/67/0a59cb257c72bb837575ca0ddf5f0fe2a482e98209b7a1bed8cde68ddb46/pandas-0.24.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting psutil (from -r requirements.txt (line 10))
  Downloading https://files.pythonhosted.org/packages/1c/ca/5b8c1fe032a458c2c4bcbe509d1401dca9dda35c7fc46b36bb81c2834740/psutil-5.6.3.tar.gz (435kB)
     |████████████████████████████████| 440kB 1.2MB/s 
Collecting pyqt5 (from -r requirements.txt (line 11))
  Using cached https://files.pythonhosted.org/packages/b8/05/0fd9de5eb664ad4c47047d857cd526576b7d45b3108fbb57ba64399be2d5/PyQt5-5.12.2-5.12.3-cp35.cp36.cp37.cp38-abi3-macosx_10_6_intel.whl
Collecting raven (from -r requirements.txt (line 12))
  Using cached https://files.pythonhosted.org/packages/bd/8e/62e26a88c0a1bbae677200baf0767c1022321a6555634f8129e6d55c5ddc/raven-6.10.0-py2.py3-none-any.whl
Collecting requests (from -r requirements.txt (line 13))
  Using cached https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl
Collecting scipy (from -r requirements.txt (line 14))
  Using cached https://files.pythonhosted.org/packages/81/ae/125c21f09b202c3009ad7d9fb0263fb7d6053813d4b67ccbbe4d65f7f53a/scipy-1.3.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting scikit-image (from -r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/c5/7c/c61e0bdb02fecd1e801d34fb534839f74055873eb935a05d96a8831d4448/scikit_image-0.15.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting scikit-learn (from -r requirements.txt (line 16))
  Using cached https://files.pythonhosted.org/packages/f2/46/4e68feb391f049b7ef9fe9bad355eecc208b3cfb324c47410580b4854cde/scikit_learn-0.21.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting tensorflow==1.3.0 (from -r requirements.txt (line 18))
  Downloading https://files.pythonhosted.org/packages/4f/8e/8f036b718c97b7a2a96f4e23fbaa55771686efaa97a56579df8d6826f7c5/tensorflow-1.3.0-cp36-cp36m-macosx_10_11_x86_64.whl (39.8MB)
     |████████████████████████████████| 39.8MB 145kB/s 
Collecting xlrd (from -r requirements.txt (line 19))
  Using cached https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl
Collecting xlutils (from -r requirements.txt (line 20))
  Using cached https://files.pythonhosted.org/packages/c7/55/e22ac73dbb316cabb5db28bef6c87044a95914f713a6e81b593f8a0d2f79/xlutils-2.0.0-py2.py3-none-any.whl
Collecting xlwt (from -r requirements.txt (line 21))
  Using cached https://files.pythonhosted.org/packages/44/48/def306413b25c3d01753603b1a222a011b8621aed27cd7f89cbc27e6b0f4/xlwt-1.3.0-py2.py3-none-any.whl
Collecting tqdm (from -r requirements.txt (line 22))
  Using cached https://files.pythonhosted.org/packages/45/af/685bf3ce889ea191f3b916557f5677cc95a5e87b2fa120d74b5dd6d049d0/tqdm-4.32.1-py2.py3-none-any.whl
Collecting transforms3d (from -r requirements.txt (line 23))
Collecting urllib3[secure] (from -r requirements.txt (line 24))
  Using cached https://files.pythonhosted.org/packages/e6/60/247f23a7121ae632d62811ba7f273d0e58972d75e58a94d329d51550a47d/urllib3-1.25.3-py2.py3-none-any.whl
Collecting nipy from git+https://github.com/jcohenadad/nipy.git#egg=nipy (from -r requirements.txt (line 25))
  Cloning https://github.com/jcohenadad/nipy.git to /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/pip-install-256prj8w/nipy
  Running command git clone -q https://github.com/jcohenadad/nipy.git /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/pip-install-256prj8w/nipy
Collecting asn1crypto>=0.21.0 (from cryptography->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting six>=1.4.1 (from cryptography->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting cffi!=1.11.3,>=1.8 (from cryptography->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/79/46/a0133536162ad7fe5ae27f22f6ed14a77132b32589dce71223ebe7e02371/cffi-1.12.3-cp36-cp36m-macosx_10_6_intel.whl
Collecting keras-preprocessing>=1.0.5 (from Keras->-r requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/28/6a/8c1f62c37212d9fc441a7e26736df51ce6f0e38455816445471f10da4f0a/Keras_Preprocessing-1.1.0-py2.py3-none-any.whl
Collecting keras-applications>=1.0.6 (from Keras->-r requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/71/e3/19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f/Keras_Applications-1.0.8-py3-none-any.whl
Collecting pyyaml (from Keras->-r requirements.txt (line 6))
Collecting cycler>=0.10 (from matplotlib->-r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->-r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/49/5d/d1726d2a2fd471a69ef5014ca42812e1ccb8a13085c42bfcb238a5611f39/kiwisolver-1.1.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->-r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/dd/d9/3ec19e966301a6e25769976999bd7bbe552016f0d32b577dc9d63d2e0c49/pyparsing-2.4.0-py2.py3-none-any.whl
Collecting python-dateutil>=2.1 (from matplotlib->-r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl
Collecting pytz>=2011k (from pandas->-r requirements.txt (line 9))
  Using cached https://files.pythonhosted.org/packages/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl
Collecting PyQt5_sip<13,>=4.19.14 (from pyqt5->-r requirements.txt (line 11))
  Using cached https://files.pythonhosted.org/packages/58/dd/177aa519d627b8cc6d2a93d69211540e81539f20234ed5b6b1f98febca34/PyQt5_sip-4.19.17-cp36-cp36m-macosx_10_6_intel.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests->-r requirements.txt (line 13))
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting idna<2.9,>=2.5 (from requests->-r requirements.txt (line 13))
  Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests->-r requirements.txt (line 13)) (2019.3.9)
Collecting networkx>=2.0 (from scikit-image->-r requirements.txt (line 15))
Collecting imageio>=2.0.1 (from scikit-image->-r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/af/0a/943c965d372dae0b1f1482677d29030ab834351a61a9a632fd62f27f1523/imageio-2.5.0-py3-none-any.whl
Collecting PyWavelets>=0.4.0 (from scikit-image->-r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/1c/66/0bdb59713833391d90b605ccf53003c41175e1fcc75dade52383cc6436b9/PyWavelets-1.0.3-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pillow>=4.3.0 (from scikit-image->-r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/68/3a/61531c34cc18f77b9f979f2cf1a670ae3e98316521e78e3f070c4cc5029b/Pillow-6.0.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting joblib>=0.11 (from scikit-learn->-r requirements.txt (line 16))
  Using cached https://files.pythonhosted.org/packages/cd/c1/50a758e8247561e58cb87305b1e90b171b8c767b15b12a1734001f41d356/joblib-0.13.2-py2.py3-none-any.whl
Collecting tensorflow-tensorboard<0.2.0,>=0.1.0 (from tensorflow==1.3.0->-r requirements.txt (line 18))
  Downloading https://files.pythonhosted.org/packages/93/31/bb4111c3141d22bd7b2b553a26aa0c1863c86cb723919e5bd7847b3de4fc/tensorflow_tensorboard-0.1.8-py3-none-any.whl (1.6MB)
     |████████████████████████████████| 1.6MB 11.8MB/s 
Collecting protobuf>=3.3.0 (from tensorflow==1.3.0->-r requirements.txt (line 18))
  Using cached https://files.pythonhosted.org/packages/2b/d9/f7a3e3fb44de98c85991fca727238c9ab8ca264e9edb2dbfd00849395d6d/protobuf-3.8.0-cp36-cp36m-macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorflow==1.3.0->-r requirements.txt (line 18)) (0.33.4)
Collecting pyOpenSSL>=0.14; extra == "secure" (from urllib3[secure]->-r requirements.txt (line 24))
  Using cached https://files.pythonhosted.org/packages/01/c8/ceb170d81bd3941cbeb9940fc6cc2ef2ca4288d0ca8929ea4db5905d904d/pyOpenSSL-19.0.0-py2.py3-none-any.whl
Collecting sympy>=0.7.0 (from nipy->-r requirements.txt (line 25))
  Using cached https://files.pythonhosted.org/packages/21/21/f4105795ca7f35c541d82c5b06be684dd2f5cb4f508fb487cd7aea4de776/sympy-1.4-py2.py3-none-any.whl
Collecting pycparser (from cffi!=1.11.3,>=1.8->cryptography->-r requirements.txt (line 2))
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)) (41.0.1)
Collecting decorator>=4.3.0 (from networkx>=2.0->scikit-image->-r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl
Collecting bleach==1.5.0 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->-r requirements.txt (line 18))
  Downloading https://files.pythonhosted.org/packages/33/70/86c5fec937ea4964184d4d6c4f0b9551564f821e1c3575907639036d9b90/bleach-1.5.0-py2.py3-none-any.whl
Collecting html5lib==0.9999999 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->-r requirements.txt (line 18))
  Downloading https://files.pythonhosted.org/packages/ae/ae/bcb60402c60932b32dfaf19bb53870b29eda2cd17551ba5639219fb5ebf9/html5lib-0.9999999.tar.gz (889kB)
     |████████████████████████████████| 890kB 13.6MB/s 
Collecting werkzeug>=0.11.10 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->-r requirements.txt (line 18))
  Using cached https://files.pythonhosted.org/packages/9f/57/92a497e38161ce40606c27a86759c6b92dd34fcdb33f64171ec559257c02/Werkzeug-0.15.4-py2.py3-none-any.whl
Collecting markdown>=2.6.8 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->-r requirements.txt (line 18))
  Using cached https://files.pythonhosted.org/packages/c0/4e/fd492e91abdc2d2fcb70ef453064d980688762079397f779758e055f6575/Markdown-3.1.1-py2.py3-none-any.whl
Collecting mpmath>=0.19 (from sympy>=0.7.0->nipy->-r requirements.txt (line 25))
Building wheels for collected packages: psutil, nipy, html5lib
  Building wheel for psutil (setup.py) ... done
  Stored in directory: /Users/shazeebm/Library/Caches/pip/wheels/90/7e/74/bb640d77775e6b6a78bcc3120f9fea4d2a28b2706de1cff37d
  Building wheel for nipy (setup.py) ... done
  Stored in directory: /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/pip-ephem-wheel-cache-2fu8uzt9/wheels/09/c5/3c/3f6341a401ac05ef0db10ca57f907769589ef12b8f35364d81
  Building wheel for html5lib (setup.py) ... done
  Stored in directory: /Users/shazeebm/Library/Caches/pip/wheels/50/ae/f9/d2b189788efcf61d1ee0e36045476735c838898eef1cad6e29
Successfully built psutil nipy html5lib
Installing collected packages: asn1crypto, six, pycparser, cffi, cryptography, nibabel, scipy, h5py, dipy, futures, keras-preprocessing, keras-applications, pyyaml, Keras, cycler, kiwisolver, pyparsing, python-dateutil, matplotlib, pytz, pandas, psutil, PyQt5-sip, pyqt5, raven, idna, pyOpenSSL, urllib3, chardet, requests, decorator, networkx, pillow, imageio, PyWavelets, scikit-image, joblib, scikit-learn, html5lib, bleach, werkzeug, protobuf, markdown, tensorflow-tensorboard, tensorflow, xlrd, xlwt, xlutils, tqdm, transforms3d, mpmath, sympy, nipy
Successfully installed Keras-2.2.4 PyQt5-sip-4.19.17 PyWavelets-1.0.3 asn1crypto-0.24.0 bleach-1.5.0 cffi-1.12.3 chardet-3.0.4 cryptography-2.7 cycler-0.10.0 decorator-4.4.0 dipy-0.16.0 futures-3.1.1 h5py-2.9.0 html5lib-0.9999999 idna-2.8 imageio-2.5.0 joblib-0.13.2 keras-applications-1.0.8 keras-preprocessing-1.1.0 kiwisolver-1.1.0 markdown-3.1.1 matplotlib-3.1.0 mpmath-1.1.0 networkx-2.3 nibabel-2.4.1 nipy-0.5.0.dev0 pandas-0.24.2 pillow-6.0.0 protobuf-3.8.0 psutil-5.6.3 pyOpenSSL-19.0.0 pycparser-2.19 pyparsing-2.4.0 pyqt5-5.12.2 python-dateutil-2.8.0 pytz-2019.1 pyyaml-5.1.1 raven-6.10.0 requests-2.22.0 scikit-image-0.15.0 scikit-learn-0.21.2 scipy-1.3.0 six-1.12.0 sympy-1.4 tensorflow-1.3.0 tensorflow-tensorboard-0.1.8 tqdm-4.32.1 transforms3d-0.3.1 urllib3-1.25.3 werkzeug-0.15.4 xlrd-1.2.0 xlutils-2.0.0 xlwt-1.3.0
Obtaining file:///Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox

Creating launchers for Python scripts...

Installing binaries...
>> sct_download_data -d binaries_osx -o /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/bin

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)

Folder /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/bin has been created.

Trying URL: https://osf.io/zjv4c/?action=download
Downloading 20181204_sct_binaries_osx.tar.gz...
Status: 100%|##############################################################################################| 68.7M/68.7M [00:08<00:00, 7.72MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/bin

Remove temporary file...
Done!

All requirements installed!
>> . /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/python/bin/activate /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/python

Installing data...
>> rm -rf /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data
>> mkdir -p /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data
>> cd /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data
>> sct_download_data -d PAM50

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/kc3jx/?action=download
Downloading 20181214_PAM50.zip...
Status: 100%|##############################################################################################| 70.8M/70.8M [00:07<00:00, 9.26MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data

Remove temporary file...
Done!

>> sct_download_data -d gm_model

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/ugscu/?action=download
Downloading 20160922_gm_model.zip...
Status: 100%|##############################################################################################| 10.3M/10.3M [00:01<00:00, 9.76MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data

Remove temporary file...
Done!

>> sct_download_data -d optic_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/g4fwn/?action=download
Downloading 20170413_optic_models.zip...
Status: 100%|##############################################################################################| 17.7k/17.7k [00:00<00:00, 2.02MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data

Remove temporary file...
Done!

>> sct_download_data -d pmj_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/4gufr/?action=download
Downloading 20170922_pmj_models.zip...
Status: 100%|##############################################################################################| 8.87k/8.87k [00:00<00:00, 8.86MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_sc_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/avf97/?action=download
Downloading 20180610_deepseg_sc_models.zip...
Status: 100%|##############################################################################################| 58.7M/58.7M [00:07<00:00, 7.61MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_gm_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/b9y4x/?action=download
Downloading 20180205_deepseg_gm_models.zip...
Status: 100%|##############################################################################################| 2.28M/2.28M [00:00<00:00, 7.51MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_lesion_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/eg7v9/?action=download
Downloading 20180613_deepseg_lesion_models.zip...
Status: 100%|##############################################################################################| 16.0M/16.0M [00:01<00:00, 9.23MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data

Remove temporary file...
Done!

>> sct_download_data -d c2c3_disc_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/t97ap/?action=download
Downloading 20190117_c2c3_disc_models.zip...
Status: 100%|##############################################################################################| 8.94k/8.94k [00:00<00:00, 9.41MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/data

Remove temporary file...
Done!


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


Validate installation...

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)

SCT info:
- version: git-master-567a67e2508704061e348d20b54cbb7963f20daa
- path: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct
OS: osx (Darwin-15.6.0-x86_64-i386-64bit)
CPU cores: Available: 2, Used by SCT: 2
RAM: Primary memory available: 4.00 gigabytes
Check Python executable.............................[OK]
  Using bundled python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] at /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.16.4)
Check if cryptography is installed..................[OK] (2.7)
Check if dipy is installed..........................[OK] (0.16.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.9.0)
Check if Keras is installed........................../install_sct: line 576: 34946 Illegal instruction: 4  sct_check_dependencies
Installation validation Failed!
Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):
http://forum.spinalcordmri.org/c/sct

Installation failed

#10

@salmanshaz could you please try to run the following (and copy/paste the output):

sct_check_dependencies
sct_testing

#11

Here it is:

ipac-imac:sct shazeebm$ sct_check_dependencies
SCT info:
- version: 4.0.0-beta.5
- path: /Users/shazeebm/sct_4.0.0-beta.5
OS: osx (Darwin-15.6.0-x86_64-i386-64bit)
CPU cores: Available: 2, Used by SCT: 2
RAM: Primary memory available: 4.00 gigabytes
Check Python executable.............................[OK]
  Using bundled python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] at /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.16.4)
Check if cryptography is installed..................[OK] (2.7)
Check if dipy is installed..........................[OK] (0.16.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.9.0)
Check if Keras is installed.........................[FAIL]
Check if matplotlib is installed....................[OK] (3.1.0)
Check if nibabel is installed.......................[OK] (2.4.1)
Check if pandas is installed........................[OK] (0.24.2)
Check if psutil is installed........................[OK] (5.6.2)
Check if pyqt5 is installed.........................[OK]
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.22.0)
Check if scipy is installed.........................[OK] (1.3.0)
Check if scikit-image is installed..................[OK] (0.15.0)
Check if scikit-learn is installed..................[OK] (0.21.2)
Check if tensorflow is installed....................[FAIL]
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] (4.32.1)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.3)
Check if git+https://github.com/jcohenadad/nipy.git is installed[OK] (0.5.0.dev)
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]

ipac-imac:sct shazeebm$ sct_testing

Trying URL: https://osf.io/z8gaj/?action=download
Downloading 20180125_sct_testing_data.zip...
Status: 100%|##############################################################################################| 6.78M/6.78M [00:02<00:00, 2.40MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct

Remove temporary file...
Done!

Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 2 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_warp_template sct_resample sct_convert sct_image sct_maths sct_merge_images 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_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_label_utils sct_process_segmentation sct_propseg sct_register_multimodal sct_straighten_spinalcord sct_register_to_template sct_smooth_spinalcord sct_label_vertebrae
Checking sct_deepseg_gm.............................[FAIL]
   
   Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613125305.651506-utc6ucyn/sct_deepseg_gm:
   ====================================================================================================
   sct_deepseg_gm -i /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/sct_testing_data/t2s/t2s_uncropped.nii.gz -igt /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/sct_testing_data/t2s/t2s_uncropped_gmseg_manual.nii.gz -o sct_deepseg_gm/output.nii.gz -qc testing-qc -m large -thr 0.999 -v 1
   ====================================================================================================
   
   Traceback (most recent call last):
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
   from tensorflow.python.pywrap_tensorflow_internal import *
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
   _pywrap_tensorflow_internal = swig_import_helper()
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
   _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
   return load_dynamic(name, filename, file)
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
   return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
   Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
   Expected in: /usr/lib/libSystem.B.dylib
   in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   
   During handling of the above exception, another exception occurred:
   
   Traceback (most recent call last):
   File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_gm.py", line 142, in <module>
   run_main()
   File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_gm.py", line 120, in run_main
   from spinalcordtoolbox.deepseg_gm import deepseg_gm
   File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_gm/deepseg_gm.py", line 30, in <module>
   from keras import backend as K
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
   from . import utils
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
   from . import conv_utils
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
   from .. import backend as K
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/__init__.py", line 89, in <module>
   from .tensorflow_backend import *
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 5, in <module>
   import tensorflow as tf
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
   from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
   from tensorflow.python import pywrap_tensorflow
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
   raise ImportError(msg)
   ImportError: Traceback (most recent call last):
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
   from tensorflow.python.pywrap_tensorflow_internal import *
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
   _pywrap_tensorflow_internal = swig_import_helper()
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
   _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
   return load_dynamic(name, filename, file)
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
   return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
   Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
   Expected in: /usr/lib/libSystem.B.dylib
   in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   
   
   Failed to load the native TensorFlow runtime.
   
   See https://www.tensorflow.org/install/errors
   
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
Checking sct_deepseg_lesion.........................[FAIL]
   Got exception: Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   
   
   Failed to load the native TensorFlow runtime.
   
   See https://www.tensorflow.org/install/errors
   
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
   Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   During handling of the above exception, another exception occurred:
   Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 495, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/importlib/__init__.py", line 126, in import_module
       return _bootstrap._gcd_import(name[level:], package, level)
     File "<frozen importlib._bootstrap>", line 994, in _gcd_import
     File "<frozen importlib._bootstrap>", line 971, in _find_and_load
     File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
     File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
     File "<frozen importlib._bootstrap_external>", line 678, in exec_module
     File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_lesion.py", line 24, in <module>
       from spinalcordtoolbox.deepseg_lesion.core import deep_segmentation_MSlesion
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_lesion/core.py", line 19, in <module>
       from spinalcordtoolbox.deepseg_sc.core import find_centerline, crop_image_around_centerline, uncrop_image, _normalize_data
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/core.py", line 14, in <module>
       from spinalcordtoolbox.deepseg_sc.cnn_models import nn_architecture_seg, nn_architecture_ctr
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/cnn_models.py", line 18, in <module>
       from keras.layers import Input, Conv2D, Conv2DTranspose
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
       from . import utils
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
       from . import conv_utils
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
       from .. import backend as K
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/__init__.py", line 89, in <module>
       from .tensorflow_backend import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 5, in <module>
       import tensorflow as tf
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
       from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
       from tensorflow.python import pywrap_tensorflow
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
       raise ImportError(msg)
   ImportError: Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   Failed to load the native TensorFlow runtime.
   See https://www.tensorflow.org/install/errors
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
Checking sct_deepseg_sc.............................[FAIL]
   Got exception: Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   
   
   Failed to load the native TensorFlow runtime.
   
   See https://www.tensorflow.org/install/errors
   
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
   Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   During handling of the above exception, another exception occurred:
   Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 495, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/importlib/__init__.py", line 126, in import_module
       return _bootstrap._gcd_import(name[level:], package, level)
     File "<frozen importlib._bootstrap>", line 994, in _gcd_import
     File "<frozen importlib._bootstrap>", line 971, in _find_and_load
     File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
     File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
     File "<frozen importlib._bootstrap_external>", line 678, in exec_module
     File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_sc.py", line 21, in <module>
       from spinalcordtoolbox.deepseg_sc.core import deep_segmentation_spinalcord
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/core.py", line 14, in <module>
       from spinalcordtoolbox.deepseg_sc.cnn_models import nn_architecture_seg, nn_architecture_ctr
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/cnn_models.py", line 18, in <module>
       from keras.layers import Input, Conv2D, Conv2DTranspose
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
       from . import utils
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
       from . import conv_utils
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
       from .. import backend as K
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/__init__.py", line 89, in <module>
       from .tensorflow_backend import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 5, in <module>
       import tensorflow as tf
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
       from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
       from tensorflow.python import pywrap_tensorflow
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
       raise ImportError(msg)
   ImportError: Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   Failed to load the native TensorFlow runtime.
   See https://www.tensorflow.org/install/errors
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
Checking sct_analyze_lesion.........................[OK]
Checking sct_analyze_texture........................[OK]
Checking sct_apply_transfo..........................[OK]
Checking sct_warp_template..........................[OK]
Checking sct_resample...............................[OK]
Checking sct_convert................................[OK]
Checking sct_image..................................[OK]
Checking sct_maths..................................[OK]
Checking sct_merge_images...........................[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_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.......................[FAIL]
   
   Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613125305.651506-utc6ucyn/sct_flatten_sagittal:
   ====================================================================================================
   sct_flatten_sagittal -i /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/sct_testing_data/t2/t2.nii.gz -s /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/sct_testing_data/t2/t2_seg.nii.gz -v 1
   ====================================================================================================
   
Checking sct_fmri_compute_tsnr......................[OK]
Checking sct_fmri_moco..............................[OK]
Checking sct_get_centerline.........................[OK]
Checking sct_label_utils............................[OK]
Checking sct_process_segmentation...................[FAIL]
   
   Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613125305.651506-utc6ucyn/sct_process_segmentation:
   ====================================================================================================
   sct_process_segmentation -i /Users/shazeebm/Desktop/spinalcordtoolbox-4.0.0-beta.5/sct/sct_testing_data/t2/t2_seg.nii.gz -vertfile ./label/template/PAM50_levels.nii.gz -r 1 -angle-corr 1 -v 1
   ====================================================================================================
   
   Compute shape analysis:   0%|                          | 0/55 [00:00<?, ?iter/s]
Checking sct_propseg................................[OK]
Checking sct_register_multimodal....................[OK]
Checking sct_straighten_spinalcord..................[OK]
Checking sct_register_to_template...................[OK]
Checking sct_smooth_spinalcord......................[OK]
Checking sct_label_vertebrae........................[OK]
status: [1, 1, 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, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0]
Failures: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc sct_flatten_sagittal sct_process_segmentation
Finished! Elapsed time: 351s

#12

Hi @salmanshaz, I meant: could you please try to run these commands using the latest master version from git, not the 4.0.0-beta.5.


#13

Sure thing. I am assuming latest master version is v3.2.7. That’s what I see in git. I installed that one and the same error appeared once it reached the Keras install part. Then I ran the last two commands with checking dependencies and the testing. The output is below. For some reason it stil says that the SCT version is the beta one. Do I have to uninstall first before installing v3.2.7? Thanks.

ipac-imac:sct shazeebm$ sct_check_dependencies
SCT info:
- version: 4.0.0-beta.5
- path: /Users/shazeebm/sct_4.0.0-beta.5
OS: osx (Darwin-15.6.0-x86_64-i386-64bit)
CPU cores: Available: 2, Used by SCT: 2
RAM: Primary memory available: 4.00 gigabytes
Check Python executable.............................[OK]
  Using bundled python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] at /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.16.4)
Check if cryptography is installed..................[OK] (2.7)
Check if dipy is installed..........................[OK] (0.16.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.9.0)
Check if Keras is installed.........................[FAIL]
Check if matplotlib is installed....................[OK] (3.1.0)
Check if nibabel is installed.......................[OK] (2.4.1)
Check if pandas is installed........................[OK] (0.24.2)
Check if psutil is installed........................[OK] (5.6.2)
Check if pyqt5 is installed.........................[OK]
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.22.0)
Check if scipy is installed.........................[OK] (1.3.0)
Check if scikit-image is installed..................[OK] (0.15.0)
Check if scikit-learn is installed..................[OK] (0.21.2)
Check if tensorflow is installed....................[FAIL]
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] (4.32.1)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.3)
Check if git+https://github.com/jcohenadad/nipy.git is installed[OK] (0.5.0.dev)
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]

ipac-imac:sct shazeebm$ sct_testing

Trying URL: https://osf.io/z8gaj/?action=download
Downloading 20180125_sct_testing_data.zip...
Status: 100%|##############################################################################################| 6.78M/6.78M [00:02<00:00, 2.91MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct

Remove temporary file...
Done!

Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 2 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_warp_template sct_resample sct_convert sct_image sct_maths sct_merge_images 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_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_label_utils sct_process_segmentation sct_propseg sct_register_multimodal sct_straighten_spinalcord sct_register_to_template sct_smooth_spinalcord sct_label_vertebrae
Checking sct_deepseg_gm.............................[FAIL]
   
   Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613152934.264374-_89ayj9o/sct_deepseg_gm:
   ====================================================================================================
   sct_deepseg_gm -i /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2s/t2s_uncropped.nii.gz -igt /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2s/t2s_uncropped_gmseg_manual.nii.gz -o sct_deepseg_gm/output.nii.gz -qc testing-qc -m large -thr 0.999 -v 1
   ====================================================================================================
   
   Traceback (most recent call last):
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
   from tensorflow.python.pywrap_tensorflow_internal import *
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
   _pywrap_tensorflow_internal = swig_import_helper()
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
   _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
   return load_dynamic(name, filename, file)
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
   return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
   Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
   Expected in: /usr/lib/libSystem.B.dylib
   in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   
   During handling of the above exception, another exception occurred:
   
   Traceback (most recent call last):
   File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_gm.py", line 142, in <module>
   run_main()
   File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_gm.py", line 120, in run_main
   from spinalcordtoolbox.deepseg_gm import deepseg_gm
   File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_gm/deepseg_gm.py", line 30, in <module>
   from keras import backend as K
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
   from . import utils
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
   from . import conv_utils
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
   from .. import backend as K
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/__init__.py", line 89, in <module>
   from .tensorflow_backend import *
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 5, in <module>
   import tensorflow as tf
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
   from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
   from tensorflow.python import pywrap_tensorflow
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
   raise ImportError(msg)
   ImportError: Traceback (most recent call last):
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
   from tensorflow.python.pywrap_tensorflow_internal import *
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
   _pywrap_tensorflow_internal = swig_import_helper()
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
   _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
   return load_dynamic(name, filename, file)
   File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
   return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
   Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
   Expected in: /usr/lib/libSystem.B.dylib
   in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   
   
   Failed to load the native TensorFlow runtime.
   
   See https://www.tensorflow.org/install/errors
   
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
Checking sct_deepseg_lesion.........................[FAIL]
   Got exception: Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   
   
   Failed to load the native TensorFlow runtime.
   
   See https://www.tensorflow.org/install/errors
   
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
   Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   During handling of the above exception, another exception occurred:
   Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 495, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/importlib/__init__.py", line 126, in import_module
       return _bootstrap._gcd_import(name[level:], package, level)
     File "<frozen importlib._bootstrap>", line 994, in _gcd_import
     File "<frozen importlib._bootstrap>", line 971, in _find_and_load
     File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
     File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
     File "<frozen importlib._bootstrap_external>", line 678, in exec_module
     File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_lesion.py", line 24, in <module>
       from spinalcordtoolbox.deepseg_lesion.core import deep_segmentation_MSlesion
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_lesion/core.py", line 19, in <module>
       from spinalcordtoolbox.deepseg_sc.core import find_centerline, crop_image_around_centerline, uncrop_image, _normalize_data
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/core.py", line 14, in <module>
       from spinalcordtoolbox.deepseg_sc.cnn_models import nn_architecture_seg, nn_architecture_ctr
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/cnn_models.py", line 18, in <module>
       from keras.layers import Input, Conv2D, Conv2DTranspose
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
       from . import utils
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
       from . import conv_utils
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
       from .. import backend as K
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/__init__.py", line 89, in <module>
       from .tensorflow_backend import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 5, in <module>
       import tensorflow as tf
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
       from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
       from tensorflow.python import pywrap_tensorflow
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
       raise ImportError(msg)
   ImportError: Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   Failed to load the native TensorFlow runtime.
   See https://www.tensorflow.org/install/errors
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
Checking sct_deepseg_sc.............................[FAIL]
   Got exception: Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   
   
   Failed to load the native TensorFlow runtime.
   
   See https://www.tensorflow.org/install/errors
   
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
   Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   During handling of the above exception, another exception occurred:
   Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 180, in process_function
       param_test = test_function(param_test)
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_testing.py", line 495, in test_function
       module_function_to_test = importlib.import_module(param_test.function_to_test)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/importlib/__init__.py", line 126, in import_module
       return _bootstrap._gcd_import(name[level:], package, level)
     File "<frozen importlib._bootstrap>", line 994, in _gcd_import
     File "<frozen importlib._bootstrap>", line 971, in _find_and_load
     File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
     File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
     File "<frozen importlib._bootstrap_external>", line 678, in exec_module
     File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
     File "/Users/shazeebm/sct_4.0.0-beta.5/scripts/sct_deepseg_sc.py", line 21, in <module>
       from spinalcordtoolbox.deepseg_sc.core import deep_segmentation_spinalcord
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/core.py", line 14, in <module>
       from spinalcordtoolbox.deepseg_sc.cnn_models import nn_architecture_seg, nn_architecture_ctr
     File "/Users/shazeebm/sct_4.0.0-beta.5/spinalcordtoolbox/deepseg_sc/cnn_models.py", line 18, in <module>
       from keras.layers import Input, Conv2D, Conv2DTranspose
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/__init__.py", line 3, in <module>
       from . import utils
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/__init__.py", line 6, in <module>
       from . import conv_utils
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in <module>
       from .. import backend as K
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/__init__.py", line 89, in <module>
       from .tensorflow_backend import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/keras/backend/tensorflow_backend.py", line 5, in <module>
       import tensorflow as tf
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/__init__.py", line 24, in <module>
       from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/__init__.py", line 49, in <module>
       from tensorflow.python import pywrap_tensorflow
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
       raise ImportError(msg)
   ImportError: Traceback (most recent call last):
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
       from tensorflow.python.pywrap_tensorflow_internal import *
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
       _pywrap_tensorflow_internal = swig_import_helper()
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
       _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module
       return load_dynamic(name, filename, file)
     File "/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic
       return _load(spec)
   ImportError: dlopen(/Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so, 6): Symbol not found: _clock_gettime
     Referenced from: /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so (which was built for Mac OS X 10.12)
     Expected in: /usr/lib/libSystem.B.dylib
    in /Users/shazeebm/sct_4.0.0-beta.5/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/../libtensorflow_framework.so
   Failed to load the native TensorFlow runtime.
   See https://www.tensorflow.org/install/errors
   for some common reasons and solutions.  Include the entire stack trace
   above this error message when asking for help.
Checking sct_analyze_lesion.........................[OK]
Checking sct_analyze_texture........................[OK]
Checking sct_apply_transfo..........................[OK]
Checking sct_warp_template..........................[OK]
Checking sct_resample...............................[OK]
Checking sct_convert................................[OK]
Checking sct_image..................................[OK]
Checking sct_maths..................................[OK]
Checking sct_merge_images...........................[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_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.......................[FAIL]
   
   Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613152934.264374-_89ayj9o/sct_flatten_sagittal:
   ====================================================================================================
   sct_flatten_sagittal -i /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2/t2.nii.gz -s /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2/t2_seg.nii.gz -v 1
   ====================================================================================================
   
Checking sct_fmri_compute_tsnr......................[OK]
Checking sct_fmri_moco..............................[OK]
Checking sct_get_centerline.........................[OK]
Checking sct_label_utils............................[OK]
Checking sct_process_segmentation...................[FAIL]
   
   Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613152934.264374-_89ayj9o/sct_process_segmentation:
   ====================================================================================================
   sct_process_segmentation -i /Users/shazeebm/Desktop/spinalcordtoolbox-3.2.7/sct/sct_testing_data/t2/t2_seg.nii.gz -vertfile ./label/template/PAM50_levels.nii.gz -r 1 -angle-corr 1 -v 1
   ====================================================================================================
   
   Compute shape analysis:   0%|                          | 0/55 [00:00<?, ?iter/s]
Checking sct_propseg................................[OK]
Checking sct_register_multimodal....................[OK]
Checking sct_straighten_spinalcord..................[OK]
Checking sct_register_to_template...................[OK]
Checking sct_smooth_spinalcord......................[OK]
Checking sct_label_vertebrae........................[OK]
status: [1, 1, 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, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0]
Failures: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc sct_flatten_sagittal sct_process_segmentation
Finished! Elapsed time: 344s

#14

I am assuming latest master version is v3.2.7. That’s what I see in git.

No, “git master” is more recent than 4.0.0-beta.5 (and de facto more recent that v3.2.7).

I installed that one and the same error appeared once it reached the Keras install part. Then I ran the last two commands with checking dependencies and the testing. The output is below. For some reason it stil says that the SCT version is the beta one. Do I have to uninstall first before installing v3.2.7? Thanks.

Indeed, you tested the 4.0.0-beta.5 again (not the latest version on from git-master). Here is what you should do:

  • open a new Terminal
  • run the following:
cd ~
git clone --branch=master https://github.com/neuropoly/spinalcordtoolbox.git sct-master
cd sct-master
yes | ./install_sct
  • Then, open a new Terminal and run the following:
sct_check_dependencies
sct_testing

And copy/paste the output.
Best,
Julien


#15

Thanks Julien. Here is the output for the first part:

ipac-imac:~ shazeebm$ cd ~
ipac-imac:~ shazeebm$ git clone --branch=master https://github.com/neuropoly/spinalcordtoolbox.git sct-master
Cloning into 'sct-master'...
remote: Enumerating objects: 246, done.
remote: Counting objects: 100% (246/246), done.
remote: Compressing objects: 100% (157/157), done.
remote: Total 43178 (delta 144), reused 156 (delta 89), pack-reused 42932
Receiving objects: 100% (43178/43178), 156.18 MiB | 4.53 MiB/s, done.
Resolving deltas: 100% (28232/28232), done.
ipac-imac:~ shazeebm$ pwd
/Users/shazeebm
ipac-imac:~ shazeebm$ ls
Applications		Library			Public
Desktop			Movies			sct-master
Documents		Music			sct_4.0.0-beta.5
Downloads		Pictures
ipac-imac:~ shazeebm$ cd sct-master/
ipac-imac:sct-master shazeebm$ yes | ./install_sct

Welcome to the SCT installer!

SCT version ......... dev
Installation type ... in-place
Operating system .... osx
Shell ............... /Users/shazeebm/.bashrc
sudo mode ........... 0

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

SCT will be installed here: [/Users/shazeebm/sct-master]
Do you agree? [y]es/[n]o: 
Skipping copy of source files (source and destination folders are the same)

Installing conda...
>> rm -rf /Users/shazeebm/sct-master/python
>> mkdir -p /Users/shazeebm/sct-master/python
>> curl -o /var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/tmp.eEAinDrL/miniconda.sh -L https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 44.0M  100 44.0M    0     0  7147k      0  0:00:06  0:00:06 --:--:-- 7694k
exit status is 0
>> bash /var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/tmp.eEAinDrL/miniconda.sh -p /Users/shazeebm/sct-master/python -b -f
PREFIX=/Users/shazeebm/sct-master/python
reinstalling: python-3.7.3-h359304d_0 ...
using -f (force) option
Python 3.7.3
reinstalling: ca-certificates-2019.1.23-0 ...
using -f (force) option
reinstalling: libcxxabi-4.0.1-hcfea43d_1 ...
using -f (force) option
reinstalling: xz-5.2.4-h1de35cc_4 ...
using -f (force) option
reinstalling: yaml-0.1.7-hc338f04_2 ...
using -f (force) option
reinstalling: zlib-1.2.11-h1de35cc_3 ...
using -f (force) option
reinstalling: libcxx-4.0.1-hcfea43d_1 ...
using -f (force) option
reinstalling: openssl-1.1.1b-h1de35cc_1 ...
using -f (force) option
reinstalling: tk-8.6.8-ha441bb4_0 ...
using -f (force) option
reinstalling: libffi-3.2.1-h475c297_4 ...
using -f (force) option
reinstalling: ncurses-6.1-h0a44026_1 ...
using -f (force) option
reinstalling: libedit-3.1.20181209-hb402a30_0 ...
using -f (force) option
reinstalling: readline-7.0-h1de35cc_5 ...
using -f (force) option
reinstalling: sqlite-3.27.2-ha441bb4_0 ...
using -f (force) option
reinstalling: asn1crypto-0.24.0-py37_0 ...
using -f (force) option
reinstalling: certifi-2019.3.9-py37_0 ...
using -f (force) option
reinstalling: chardet-3.0.4-py37_1 ...
using -f (force) option
reinstalling: idna-2.8-py37_0 ...
using -f (force) option
reinstalling: pycosat-0.6.3-py37h1de35cc_0 ...
using -f (force) option
reinstalling: pycparser-2.19-py37_0 ...
using -f (force) option
reinstalling: pysocks-1.6.8-py37_0 ...
using -f (force) option
reinstalling: python.app-2-py37_9 ...
using -f (force) option
reinstalling: ruamel_yaml-0.15.46-py37h1de35cc_0 ...
using -f (force) option
reinstalling: six-1.12.0-py37_0 ...
using -f (force) option
reinstalling: cffi-1.12.2-py37hb5b8e2f_1 ...
using -f (force) option
reinstalling: setuptools-41.0.0-py37_0 ...
using -f (force) option
reinstalling: cryptography-2.6.1-py37ha12b0ac_0 ...
using -f (force) option
reinstalling: wheel-0.33.1-py37_0 ...
using -f (force) option
reinstalling: pip-19.0.3-py37_0 ...
using -f (force) option
reinstalling: pyopenssl-19.0.0-py37_0 ...
using -f (force) option
reinstalling: urllib3-1.24.1-py37_0 ...
using -f (force) option
reinstalling: requests-2.21.0-py37_0 ...
using -f (force) option
reinstalling: conda-4.6.14-py37_0 ...
using -f (force) option
using -f (force) option
installation finished.
Conda installation successful
Collecting package metadata: done
Solving environment: done

## Package Plan ##

  environment location: /Users/shazeebm/sct-master/python/envs/venv_sct

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2019.5.15  |                0         133 KB
    certifi-2019.3.9           |           py36_0         155 KB
    openssl-1.1.1c             |       h1de35cc_1         3.4 MB
    pip-19.1.1                 |           py36_0         1.9 MB
    python-3.6.8               |       haf84260_0        20.5 MB
    setuptools-41.0.1          |           py36_0         641 KB
    sqlite-3.28.0              |       ha441bb4_0         2.3 MB
    wheel-0.33.4               |           py36_0          39 KB
    ------------------------------------------------------------
                                           Total:        29.1 MB

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2019.5.15-0
  certifi            pkgs/main/osx-64::certifi-2019.3.9-py36_0
  libcxx             pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
  libcxxabi          pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.2.1-h475c297_4
  ncurses            pkgs/main/osx-64::ncurses-6.1-h0a44026_1
  openssl            pkgs/main/osx-64::openssl-1.1.1c-h1de35cc_1
  pip                pkgs/main/osx-64::pip-19.1.1-py36_0
  python             pkgs/main/osx-64::python-3.6.8-haf84260_0
  readline           pkgs/main/osx-64::readline-7.0-h1de35cc_5
  setuptools         pkgs/main/osx-64::setuptools-41.0.1-py36_0
  sqlite             pkgs/main/osx-64::sqlite-3.28.0-ha441bb4_0
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  wheel              pkgs/main/osx-64::wheel-0.33.4-py36_0
  xz                 pkgs/main/osx-64::xz-5.2.4-h1de35cc_4
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Proceed ([y]/n)? 

Downloading and Extracting Packages
certifi-2019.3.9     | 155 KB    | ########################################## | 100% 
pip-19.1.1           | 1.9 MB    | ########################################## | 100% 
sqlite-3.28.0        | 2.3 MB    | ########################################## | 100% 
python-3.6.8         | 20.5 MB   | ########################################## | 100% 
ca-certificates-2019 | 133 KB    | ########################################## | 100% 
openssl-1.1.1c       | 3.4 MB    | ########################################## | 100% 
setuptools-41.0.1    | 641 KB    | ########################################## | 100% 
wheel-0.33.4         | 39 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 https://files.pythonhosted.org/packages/0f/c9/3526a357b6c35e5529158fbcfac1bb3adc8827e8809a6d254019d326d1cc/numpy-1.16.4-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Installing collected packages: numpy
Successfully installed numpy-1.16.4
Ignoring tensorflow: markers 'platform_system != "Darwin" or "15." not 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)) (1.16.4)
Collecting cryptography (from -r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/63/4e/57b7a6bd98906872fcd2531e74b532de2abe17d675a5cf171931fcb4a9e8/cryptography-2.7-cp34-abi3-macosx_10_6_intel.whl
Collecting dipy (from -r requirements.txt (line 3))
  Using cached https://files.pythonhosted.org/packages/62/8f/63fe5e03244b0044307bcb9742df367ebcd6b00220c7ce1d16150fd5bcdb/dipy-0.16.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting futures (from -r requirements.txt (line 4))
Collecting h5py (from -r requirements.txt (line 5))
  Using cached https://files.pythonhosted.org/packages/03/21/1cdf7fa7868528b35c1a08a770eb9334279574a8b5f1d7a2966dcec14e42/h5py-2.9.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting Keras (from -r requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/5e/10/aa32dad071ce52b5502266b5c659451cfd6ffcbf14e6c8c4f16c0ff5aaab/Keras-2.2.4-py2.py3-none-any.whl
Collecting matplotlib (from -r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/45/bf/8d8233749b5f8580bdfdb2aeed0d2df177daab44cfebc5c0de827ce1b11e/matplotlib-3.1.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting nibabel (from -r requirements.txt (line 8))
  Using cached https://files.pythonhosted.org/packages/66/30/fbed62172920c3fd050b6483541546a87c5e735f4a0ef03f08bb150680b4/nibabel-2.4.1-py2.py3-none-any.whl
Collecting pandas (from -r requirements.txt (line 9))
  Using cached https://files.pythonhosted.org/packages/2a/67/0a59cb257c72bb837575ca0ddf5f0fe2a482e98209b7a1bed8cde68ddb46/pandas-0.24.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting psutil (from -r requirements.txt (line 10))
Collecting pyqt5 (from -r requirements.txt (line 11))
  Using cached https://files.pythonhosted.org/packages/b8/05/0fd9de5eb664ad4c47047d857cd526576b7d45b3108fbb57ba64399be2d5/PyQt5-5.12.2-5.12.3-cp35.cp36.cp37.cp38-abi3-macosx_10_6_intel.whl
Collecting raven (from -r requirements.txt (line 12))
  Using cached https://files.pythonhosted.org/packages/bd/8e/62e26a88c0a1bbae677200baf0767c1022321a6555634f8129e6d55c5ddc/raven-6.10.0-py2.py3-none-any.whl
Collecting requests (from -r requirements.txt (line 13))
  Using cached https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl
Collecting scipy (from -r requirements.txt (line 14))
  Using cached https://files.pythonhosted.org/packages/81/ae/125c21f09b202c3009ad7d9fb0263fb7d6053813d4b67ccbbe4d65f7f53a/scipy-1.3.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting scikit-image (from -r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/c5/7c/c61e0bdb02fecd1e801d34fb534839f74055873eb935a05d96a8831d4448/scikit_image-0.15.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting scikit-learn (from -r requirements.txt (line 16))
  Using cached https://files.pythonhosted.org/packages/f2/46/4e68feb391f049b7ef9fe9bad355eecc208b3cfb324c47410580b4854cde/scikit_learn-0.21.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting tensorflow==1.3.0 (from -r requirements.txt (line 18))
  Using cached https://files.pythonhosted.org/packages/4f/8e/8f036b718c97b7a2a96f4e23fbaa55771686efaa97a56579df8d6826f7c5/tensorflow-1.3.0-cp36-cp36m-macosx_10_11_x86_64.whl
Collecting xlrd (from -r requirements.txt (line 19))
  Using cached https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl
Collecting xlutils (from -r requirements.txt (line 20))
  Using cached https://files.pythonhosted.org/packages/c7/55/e22ac73dbb316cabb5db28bef6c87044a95914f713a6e81b593f8a0d2f79/xlutils-2.0.0-py2.py3-none-any.whl
Collecting xlwt (from -r requirements.txt (line 21))
  Using cached https://files.pythonhosted.org/packages/44/48/def306413b25c3d01753603b1a222a011b8621aed27cd7f89cbc27e6b0f4/xlwt-1.3.0-py2.py3-none-any.whl
Collecting tqdm (from -r requirements.txt (line 22))
  Using cached https://files.pythonhosted.org/packages/45/af/685bf3ce889ea191f3b916557f5677cc95a5e87b2fa120d74b5dd6d049d0/tqdm-4.32.1-py2.py3-none-any.whl
Collecting transforms3d (from -r requirements.txt (line 23))
Collecting urllib3[secure] (from -r requirements.txt (line 24))
  Using cached https://files.pythonhosted.org/packages/e6/60/247f23a7121ae632d62811ba7f273d0e58972d75e58a94d329d51550a47d/urllib3-1.25.3-py2.py3-none-any.whl
Collecting nipy from git+https://github.com/jcohenadad/nipy.git#egg=nipy (from -r requirements.txt (line 25))
  Cloning https://github.com/jcohenadad/nipy.git to /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/pip-install-td7g3vkt/nipy
  Running command git clone -q https://github.com/jcohenadad/nipy.git /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/pip-install-td7g3vkt/nipy
Collecting asn1crypto>=0.21.0 (from cryptography->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/ea/cd/35485615f45f30a510576f1a56d1e0a7ad7bd8ab5ed7cdc600ef7cd06222/asn1crypto-0.24.0-py2.py3-none-any.whl
Collecting cffi!=1.11.3,>=1.8 (from cryptography->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/79/46/a0133536162ad7fe5ae27f22f6ed14a77132b32589dce71223ebe7e02371/cffi-1.12.3-cp36-cp36m-macosx_10_6_intel.whl
Collecting six>=1.4.1 (from cryptography->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting keras-preprocessing>=1.0.5 (from Keras->-r requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/28/6a/8c1f62c37212d9fc441a7e26736df51ce6f0e38455816445471f10da4f0a/Keras_Preprocessing-1.1.0-py2.py3-none-any.whl
Collecting pyyaml (from Keras->-r requirements.txt (line 6))
Collecting keras-applications>=1.0.6 (from Keras->-r requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/71/e3/19762fdfc62877ae9102edf6342d71b28fbfd9dea3d2f96a882ce099b03f/Keras_Applications-1.0.8-py3-none-any.whl
Collecting cycler>=0.10 (from matplotlib->-r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
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  Using cached https://files.pythonhosted.org/packages/dd/d9/3ec19e966301a6e25769976999bd7bbe552016f0d32b577dc9d63d2e0c49/pyparsing-2.4.0-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib->-r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/49/5d/d1726d2a2fd471a69ef5014ca42812e1ccb8a13085c42bfcb238a5611f39/kiwisolver-1.1.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting python-dateutil>=2.1 (from matplotlib->-r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl
Collecting pytz>=2011k (from pandas->-r requirements.txt (line 9))
  Using cached https://files.pythonhosted.org/packages/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl
Collecting PyQt5_sip<13,>=4.19.14 (from pyqt5->-r requirements.txt (line 11))
  Using cached https://files.pythonhosted.org/packages/58/dd/177aa519d627b8cc6d2a93d69211540e81539f20234ed5b6b1f98febca34/PyQt5_sip-4.19.17-cp36-cp36m-macosx_10_6_intel.whl
Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests->-r requirements.txt (line 13)) (2019.3.9)
Collecting chardet<3.1.0,>=3.0.2 (from requests->-r requirements.txt (line 13))
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting idna<2.9,>=2.5 (from requests->-r requirements.txt (line 13))
  Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl
Collecting imageio>=2.0.1 (from scikit-image->-r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/af/0a/943c965d372dae0b1f1482677d29030ab834351a61a9a632fd62f27f1523/imageio-2.5.0-py3-none-any.whl
Collecting networkx>=2.0 (from scikit-image->-r requirements.txt (line 15))
Collecting PyWavelets>=0.4.0 (from scikit-image->-r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/1c/66/0bdb59713833391d90b605ccf53003c41175e1fcc75dade52383cc6436b9/PyWavelets-1.0.3-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pillow>=4.3.0 (from scikit-image->-r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/68/3a/61531c34cc18f77b9f979f2cf1a670ae3e98316521e78e3f070c4cc5029b/Pillow-6.0.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting joblib>=0.11 (from scikit-learn->-r requirements.txt (line 16))
  Using cached https://files.pythonhosted.org/packages/cd/c1/50a758e8247561e58cb87305b1e90b171b8c767b15b12a1734001f41d356/joblib-0.13.2-py2.py3-none-any.whl
Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorflow==1.3.0->-r requirements.txt (line 18)) (0.33.4)
Collecting tensorflow-tensorboard<0.2.0,>=0.1.0 (from tensorflow==1.3.0->-r requirements.txt (line 18))
  Using cached https://files.pythonhosted.org/packages/93/31/bb4111c3141d22bd7b2b553a26aa0c1863c86cb723919e5bd7847b3de4fc/tensorflow_tensorboard-0.1.8-py3-none-any.whl
Collecting protobuf>=3.3.0 (from tensorflow==1.3.0->-r requirements.txt (line 18))
  Using cached https://files.pythonhosted.org/packages/2b/d9/f7a3e3fb44de98c85991fca727238c9ab8ca264e9edb2dbfd00849395d6d/protobuf-3.8.0-cp36-cp36m-macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pyOpenSSL>=0.14; extra == "secure" (from urllib3[secure]->-r requirements.txt (line 24))
  Using cached https://files.pythonhosted.org/packages/01/c8/ceb170d81bd3941cbeb9940fc6cc2ef2ca4288d0ca8929ea4db5905d904d/pyOpenSSL-19.0.0-py2.py3-none-any.whl
Collecting sympy>=0.7.0 (from nipy->-r requirements.txt (line 25))
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Collecting pycparser (from cffi!=1.11.3,>=1.8->cryptography->-r requirements.txt (line 2))
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)) (41.0.1)
Collecting decorator>=4.3.0 (from networkx>=2.0->scikit-image->-r requirements.txt (line 15))
  Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl
Collecting html5lib==0.9999999 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->-r requirements.txt (line 18))
Collecting werkzeug>=0.11.10 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->-r requirements.txt (line 18))
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Collecting markdown>=2.6.8 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->-r requirements.txt (line 18))
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Collecting mpmath>=0.19 (from sympy>=0.7.0->nipy->-r requirements.txt (line 25))
Building wheels for collected packages: nipy
  Building wheel for nipy (setup.py) ... done
  Stored in directory: /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/pip-ephem-wheel-cache-gzyl_bs5/wheels/09/c5/3c/3f6341a401ac05ef0db10ca57f907769589ef12b8f35364d81
Successfully built nipy
Installing collected packages: asn1crypto, pycparser, cffi, six, cryptography, scipy, h5py, nibabel, dipy, futures, keras-preprocessing, pyyaml, keras-applications, Keras, cycler, pyparsing, kiwisolver, python-dateutil, matplotlib, pytz, pandas, psutil, PyQt5-sip, pyqt5, raven, chardet, idna, pyOpenSSL, urllib3, requests, pillow, imageio, decorator, networkx, PyWavelets, scikit-image, joblib, scikit-learn, html5lib, werkzeug, bleach, protobuf, markdown, tensorflow-tensorboard, tensorflow, xlrd, xlwt, xlutils, tqdm, transforms3d, mpmath, sympy, nipy
Successfully installed Keras-2.2.4 PyQt5-sip-4.19.17 PyWavelets-1.0.3 asn1crypto-0.24.0 bleach-1.5.0 cffi-1.12.3 chardet-3.0.4 cryptography-2.7 cycler-0.10.0 decorator-4.4.0 dipy-0.16.0 futures-3.1.1 h5py-2.9.0 html5lib-0.9999999 idna-2.8 imageio-2.5.0 joblib-0.13.2 keras-applications-1.0.8 keras-preprocessing-1.1.0 kiwisolver-1.1.0 markdown-3.1.1 matplotlib-3.1.0 mpmath-1.1.0 networkx-2.3 nibabel-2.4.1 nipy-0.5.0.dev0 pandas-0.24.2 pillow-6.0.0 protobuf-3.8.0 psutil-5.6.3 pyOpenSSL-19.0.0 pycparser-2.19 pyparsing-2.4.0 pyqt5-5.12.2 python-dateutil-2.8.0 pytz-2019.1 pyyaml-5.1.1 raven-6.10.0 requests-2.22.0 scikit-image-0.15.0 scikit-learn-0.21.2 scipy-1.3.0 six-1.12.0 sympy-1.4 tensorflow-1.3.0 tensorflow-tensorboard-0.1.8 tqdm-4.32.1 transforms3d-0.3.1 urllib3-1.25.3 werkzeug-0.15.4 xlrd-1.2.0 xlutils-2.0.0 xlwt-1.3.0
Obtaining file:///Users/shazeebm/sct-master
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox

Creating launchers for Python scripts...

Installing binaries...
>> sct_download_data -d binaries_osx -o /Users/shazeebm/sct-master/bin

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)

Folder /Users/shazeebm/sct-master/bin has been created.

Trying URL: https://osf.io/zjv4c/?action=download
Downloading 20181204_sct_binaries_osx.tar.gz...
Status: 100%|###################################| 68.7M/68.7M [00:22<00:00, 3.12MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/sct-master/bin

Remove temporary file...
Done!

All requirements installed!
>> . /Users/shazeebm/sct-master/python/bin/activate /Users/shazeebm/sct-master/python

Installing data...
>> rm -rf /Users/shazeebm/sct-master/data
>> mkdir -p /Users/shazeebm/sct-master/data
>> cd /Users/shazeebm/sct-master/data
>> sct_download_data -d PAM50

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/kc3jx/?action=download
Downloading 20181214_PAM50.zip...
Status: 100%|###################################| 70.8M/70.8M [00:12<00:00, 5.86MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/sct-master/data

Remove temporary file...
Done!

>> sct_download_data -d gm_model

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/ugscu/?action=download
Downloading 20160922_gm_model.zip...
Status: 100%|###################################| 10.3M/10.3M [00:01<00:00, 8.28MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/sct-master/data

Remove temporary file...
Done!

>> sct_download_data -d optic_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/g4fwn/?action=download
Downloading 20170413_optic_models.zip...
Status: 100%|###################################| 17.7k/17.7k [00:00<00:00, 2.71MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/sct-master/data

Remove temporary file...
Done!

>> sct_download_data -d pmj_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/4gufr/?action=download
Downloading 20170922_pmj_models.zip...
Status: 100%|###################################| 8.87k/8.87k [00:00<00:00, 8.80MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/sct-master/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_sc_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/avf97/?action=download
Downloading 20180610_deepseg_sc_models.zip...
Status: 100%|###################################| 58.7M/58.7M [00:07<00:00, 8.20MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/sct-master/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_gm_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/b9y4x/?action=download
Downloading 20180205_deepseg_gm_models.zip...
Status: 100%|###################################| 2.28M/2.28M [00:00<00:00, 5.03MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/sct-master/data

Remove temporary file...
Done!

>> sct_download_data -d deepseg_lesion_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/eg7v9/?action=download
Downloading 20180613_deepseg_lesion_models.zip...
Status: 100%|###################################| 16.0M/16.0M [00:02<00:00, 5.37MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/sct-master/data

Remove temporary file...
Done!

>> sct_download_data -d c2c3_disc_models

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)


Trying URL: https://osf.io/t97ap/?action=download
Downloading 20190117_c2c3_disc_models.zip...
Status: 100%|###################################| 8.94k/8.94k [00:00<00:00, 7.51MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm/sct-master/data

Remove temporary file...
Done!


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

Validate installation...

--
Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)

SCT info:
- version: git-master-567a67e2508704061e348d20b54cbb7963f20daa
- path: /Users/shazeebm/sct-master
OS: osx (Darwin-15.6.0-x86_64-i386-64bit)
CPU cores: Available: 2, Used by SCT: 2
RAM: Primary memory available: 4.00 gigabytes
Check Python executable.............................[OK]
  Using bundled python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] at /Users/shazeebm/sct-master/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.16.4)
Check if cryptography is installed..................[OK] (2.7)
Check if dipy is installed..........................[OK] (0.16.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.9.0)
Check if Keras is installed........................../install_sct: line 576: 42891 Illegal instruction: 4  sct_check_dependencies
Installation validation Failed!
Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):
http://forum.spinalcordmri.org/c/sct

Installation failed

#16

Here is the second part:

ipac-imac:~ shazeebm$ sct_check_dependencies

--

Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)

SCT info:

- version: git-master-567a67e2508704061e348d20b54cbb7963f20daa

- path: /Users/shazeebm/sct-master

OS: osx (Darwin-15.6.0-x86_64-i386-64bit)

CPU cores: Available: 2, Used by SCT: 2

RAM: Primary memory available: 4.00 gigabytes

Check Python executable.............................[OK]

Using bundled python 3.6.8 |Anaconda, Inc.| (default, Dec 29 2018, 19:04:46) 

[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] at /Users/shazeebm/sct-master/python/envs/venv_sct/bin/python

Check if data are installed.........................[OK]

Check if numpy is installed.........................[OK] (1.16.4)

Check if cryptography is installed..................[OK] (2.7)

Check if dipy is installed..........................[OK] (0.16.0)

Check if futures is installed.......................[OK]

Check if h5py is installed..........................[OK] (2.9.0)

Check if Keras is installed.........................Illegal instruction: 4

ipac-imac:~ shazeebm$ sct_testing

--

Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)

Trying URL: https://osf.io/z8gaj/?action=download

Downloading 20180125_sct_testing_data.zip...

Status: 100%|##############################| 6.78M/6.78M [00:00&lt;00:00, 8.19MB/s]

Check if folder already exists...

Unzip data to: /Users/shazeebm

Remove temporary file...

Done!

Will run through the following tests:

- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc

- in parallel with 2 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_warp_template sct_resample sct_convert sct_image sct_maths sct_merge_images 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_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_label_utils sct_process_segmentation sct_propseg sct_register_multimodal sct_straighten_spinalcord sct_register_to_template sct_smooth_spinalcord sct_label_vertebrae

Checking sct_deepseg_gm.............................[FAIL]

Will run in /private/var/folders/ll/f4rl6yt579v_gh0rjj_gm6c80000gn/T/sct-20190613163655.484050-_05k8uue/sct_deepseg_gm:

====================================================================================================

sct_deepseg_gm -i /Users/shazeebm/sct_testing_data/t2s/t2s_uncropped.nii.gz -igt /Users/shazeebm/sct_testing_data/t2s/t2s_uncropped_gmseg_manual.nii.gz -o sct_deepseg_gm/output.nii.gz -qc testing-qc -m large -thr 0.999 -v 1

====================================================================================================

--

Spinal Cord Toolbox (git-master-567a67e2508704061e348d20b54cbb7963f20daa)

Checking sct_deepseg_lesion.........................Illegal instruction: 4

ipac-imac:~ shazeebm$

#17

Thank you @salmanshaz, I should have all the information I need to find out what the problem is.


#18

Great, thanks! Looking forward to using this software.


#19

Sorry I might need more info from your end. Could you please run the following and send me the output:

cd ~/sct-master
source python/etc/profile.d/conda.sh 
conda activate python/envs/venv_sct/
python -c 'import keras; print(keras.__version__)'

#20

No problem at all. Here it is:

ipac-imac:~ shazeebm$ cd ~/sct-master

ipac-imac:sct-master shazeebm$ source python/etc/profile.d/conda.sh

ipac-imac:sct-master shazeebm$ conda activate python/envs/venv_sct/

(venv_sct) ipac-imac:sct-master shazeebm$ python -c 'import keras; print(keras.__version__)'

Using TensorFlow backend.

Illegal instruction: 4