Installation for Linux¶

Warning

If you use Windows Subsystem for Linux (WSL), please refer to the Windows installation section.

Requirements¶

Supported Operating Systems¶

Debian >=9
Ubuntu >= 16.04
Fedora >= 19
RedHat/CentOS >= 7

Gnu Compiler Collection (gcc)¶

You need to have gcc installed. We recommend installing it via your package manager.

For example on Debian/Ubuntu:

apt install gcc

On CentOS/RedHat:

yum -y install gcc

Installation Options¶

Option 1: Install from Package (recommended)¶

The simplest way to install SCT is to do it via a stable release. First, download the latest release. Major changes to each release are listed in the Changelog.

Once you have downloaded SCT, unpack it (note: Safari will automatically unzip it). Then, open a new Terminal, go into the created folder and launch the installer:

./install_sct

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.

Retrieve the SCT code

Clone the repository and hop inside:

git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox

cd spinalcordtoolbox

(Optional) Checkout the revision of interest, if different from master:
```
git checkout ${revision_of_interest}
```
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:

Retrieve the SCT code to a safe place

Clone the repository and hop inside:

git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox

cd spinalcordtoolbox

Checkout the revision of interest, if different from master:
```
git checkout ${revision_of_interest}
```
If numpy is not already on the system, install it, either using your distribution package manager or pip.
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. Then, follow the examples below to create an OS-specific SCT installation.

Docker Image: Ubuntu¶

# Start from the Terminal
docker pull ubuntu:16.04
# Launch interactive mode (command-line inside container)
docker run -it ubuntu
# Now, inside Docker container, install dependencies
apt-get update
apt install -y git curl bzip2 libglib2.0-0 gcc
# Note for above: libglib2.0-0 is required by PyQt
# Install SCT
git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox.git sct
cd sct
./install_sct -y
export PATH="/sct/bin:${PATH}"
# Test SCT
sct_testing
# save the state of the container. Open a new Terminal and run:
docker ps -a  # list all containers
docker commit <CONTAINER_ID> <YOUR_NAME>/ubuntu:ubuntu16.04

Docker Image: CentOS7¶

# Start from the Terminal
docker pull centos:centos7
# Launch interactive mode (command-line inside container)
docker run -it centos:centos7
# Now, inside Docker container, install dependencies
yum install -y which gcc git curl
# Install SCT
git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox.git sct
cd sct
./install_sct -y
export PATH="/sct/bin:${PATH}"
# Test SCT
sct_testing
# save the state of the container. Open a new Terminal and run:
docker ps -a  # list all containers
docker commit <CONTAINER_ID> <YOUR_NAME>/centos:centos7

Enable GUI Scripts (Optional)¶

In order to run scripts with GUI you need to allow X11 redirection. First, save your Docker image:

Open another Terminal
List current docker images
```
docker ps -a
```

Save container as new image

docker commit <CONTAINER_ID> <YOUR_NAME>/<DISTROS>:<VERSION>

Create an X11 server for handling display:

Install XQuartz X11 server.
Check ‘Allow connections from network clientsoption inXQuartz` settings.
Quit and restart XQuartz.
In XQuartz window xhost + 127.0.0.1
In your other Terminal window, run: docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix <CONTAINER_ID>

Option 5: Hard-core Installation-less SCT usage¶

This is completely unsupported.

Procedure:

Retrieve the SCT code

Install dependencies

Example for Ubuntu 18.04:

# The less obscure ones may be packaged in the distribution
sudo apt install python3-{numpy,scipy,nibabel,matplotlib,h5py,mpi4py,keras,tqdm,sympy,requests,sklearn,skimage}
# The more obscure ones would be on pip
sudo apt install libmpich-dev
pip3 install --user distribute2mpi nipy dipy

Example for Debian 8 Jessie:

# The less obscure ones may be packaged in the distribution
sudo apt install python3-{numpy,scipy,matplotlib,h5py,mpi4py,requests}
# The more obscure ones would be on pip
sudo apt install libmpich-dev
pip3 install --user distribute2mpi sympy tqdm Keras nibabel nipy dipy scikit-image sklearn

Prepare the runtime environment

# Create launcher-less scripts
mkdir -p bin
find scripts/ -executable | while read file; do ln -sf "../${file}" "bin/$(basename ${file//.py/})"; done
PATH+=":$PWD/bin"

# Download binary programs
mkdir bins
pushd bins
sct_download_data -d binaries_linux
popd
PATH+=":$PWD/bins"

# Download models & cie
mkdir data; pushd data; for x in PAM50 optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models deepreg_models ; do sct_download_data -d $x; done; popd

# Add path to spinalcordtoolbox to PYTHONPATH
export PYTHONPATH="$PWD:$PWD/scripts"