SpinalCordToolbox

Comprehensive and open-source library of analysis tools for MRI of the spinal cord.

Installation

see: https://sourceforge.net/p/spinalcordtoolbox/wiki/installation/

List of tools

see: http://sourceforge.net/p/spinalcordtoolbox/wiki/tools/

Get started

see: https://sourceforge.net/p/spinalcordtoolbox/wiki/get_started/

License

All files are licensed as described in the LICENSE.TXT file.

Environment variable

If you install the toolbox from GitHub, DO NOT RUN THE INSTALLER. The installer is only made for packages (created by create_package.py). So, if you get the toolbox from GitHub, you need to edite your .bash_profile accordingly:

# SPINALCORDTOOLBOX
SCT_DIR="path_to_the_toolbox"
export PATH=${PATH}:$SCT_DIR/scripts
export PATH=${PATH}:$SCT_DIR/bin/osx
export SCT_DIR PATH
export PATH=${PATH}:$SCT_DIR/install/osx/ants
export PATH=${PATH}:$SCT_DIR/install/osx/c3d

N.B. If you are running debian/ubuntu, replace "osx" by "debian"