Installation for MacOS#

Requirements#

Supported Operating Systems#

  • MacOS >= 10.13

Mac computers with Apple silicon#

If your computer uses Apple silicon (M1, M2, M3, etc.), you need to make sure Rosetta 2 is installed before installing or running SCT. To do this, you can open a Terminal and run:

softwareupdate --install-rosetta

Gnu Compiler Collection (gcc)#

You need to have gcc installed. Check to see if gcc is installed by opening a Terminal and running:

gcc --version

If it isn’t installed, we recommend installing Homebrew and then run:

brew install gcc

Installation Options#

Option 2: Install from GitHub (development)#

If you wish to benefit from the cutting-edge version of SCT, or if you wish to contribute to the code, we recommend you download the GitHub version.

  1. Retrieve the SCT code

    Clone the repository and hop inside:

    git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox
    
    cd spinalcordtoolbox
    
  2. (Optional) Checkout the revision of interest, if different from master:

    git checkout ${revision_of_interest}
    
  3. Run the installer and follow the instructions

    ./install_sct
    

Option 3: Install with pip (experimental)#

SCT can be installed using pip, with some caveats:

  • The installation is done in-place, so the folder containing SCT must be kept around

  • In order to ensure coexistence with other packages, the dependency specifications are loosened, and it is possible that your package combination has not been tested with SCT.

    So in case of problems, try again with the reference installation, and report a bug indicating the dependency versions retrieved using sct_check_dependencies.

Procedure:

  1. Retrieve the SCT code to a safe place

    Clone the repository and hop inside:

    git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox
    
    cd spinalcordtoolbox
    
  2. Checkout the revision of interest, if different from master:

    git checkout ${revision_of_interest}
    
  3. If numpy is not already on the system, install it, either using your distribution package manager or pip.

  4. Install sct using pip

    If running in a virtualenv:

    pip install -e .
    

    else:

    pip install --user -e .
    

Option 4: Install with Docker#

Docker is a portable (Linux, macOS, Windows) container platform.

In the context of SCT, it can be used:

  • To run SCT on Windows, until SCT can run natively there

  • For development testing of SCT, faster than running a full-fledged virtual machine

  • <your reason here>

Basic Installation (No GUI)#

First, install Docker Desktop. Then, follow the examples below to create an OS-specific SCT installation.

Docker Image: Ubuntu#

First, launch Docker Desktop, then open up a new Terminal window and run the commands below:

# Start from the Terminal
docker pull ubuntu:22.04
# If the previous command says 'Cannot connect to the Docker daemon', make sure you have launched Docker Desktop
# Launch interactive mode (command-line inside container)
docker run -it ubuntu:22.04
# Now, inside Docker container, install dependencies
apt-get update
apt install -y git curl bzip2 libglib2.0-0 libgl1-mesa-glx libxrender1 libxkbcommon-x11-0 libdbus-1-3 gcc
# Note for above: libglib2.0-0, libgl1-mesa-glx, libxrender1, libxkbcommon-x11-0, libdbus-1-3 are required by PyQt
# Install SCT
git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox.git sct
cd sct
./install_sct -y
# For the previous command, it's normal if the last two checks show [FAIL] in red
# This will be fixed by doing the "Enable GUI Scripts" optional step in the next section
source /root/.bashrc
# Test SCT
sct_testing
# Save the state of the container as a docker image.
# Back on the Host machine, open a new terminal and run:
docker ps -a  # list all containers (to find out the container ID)
# specify the ID, and also choose a name to use for the docker image, such as "sct_v6.0"
docker commit <CONTAINER_ID> <IMAGE_NAME>/ubuntu:ubuntu22.04

Enable GUI Scripts (Optional)#

In order to run scripts with GUI you need to allow X11 redirection. First, save your Docker image if you haven’t already done so:

  1. Open another Terminal

  2. List current docker images

    docker ps -a
    
  3. Save container as new image

    docker commit <CONTAINER_ID> <IMAGE_NAME>/ubuntu:ubuntu22.04
    

Create an X11 server for handling display:

  1. Install XQuartz X11 server.

  2. Check ‘Allow connections from network clients option in XQuartz` settings. (Run XQuartz; in the top-of-screen menu bar, choose “XQuartz”, then “Preferences…”; the relevant option is under the “Security” tab.)

  3. Quit and restart XQuartz.

  4. In the XQuartz “xterm” window, run the command:

    xhost + 127.0.0.1
    
  5. In your other Terminal window, run:

    docker run -e DISPLAY=host.docker.internal:0 -it <IMAGE_NAME>/ubuntu:ubuntu22.04
    

    (If this command says ‘Cannot connect to the Docker daemon’, try again after launching Docker Desktop.)

  6. You can test whether GUI scripts are available by running the following command in your Docker container:

    sct_check_dependencies
    

    You should see two green [OK] symbols at the bottom of the report for “PyQT” and “matplotlib” checks, which represent the GUI features provided by SCT.

Additional Notes#

If MATLAB is Installed#

MATLAB took the liberty of setting DYLD_LIBRARY_PATH and in order for SCT to run, you have to run:

setenv('DYLD_LIBRARY_PATH', '');

Prior to running SCT commands. See https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/405