Table Of Contents

Get Started

Install the software

Before you can start using the MIRTK or develop your own MIRTK applications, you have to install the desired modules and available applications on your system including their prerequisites. For a manual installation of the MIRTK, please follow the Download and Installation instructions which list the third-party libraries required by each module and describe how to build the MIRTK from its publicly available source code.

Instead of manually installing the MIRTK locally on your system, you can use the pre-made biomedia/mirtk Docker image to run the Applications inside a Docker container.

For a guide to install and use Docker, see the official docs.

Bash completion

For information on how to enable auto-completion when running mirtk commands of a manual MIRTK installation in the Bash shell, see the Installation instructions.

To enable Bash completion for running the MIRTK commands with Docker, copy the docker and docker-mirtk completion scripts to /etc/bash_completion.d/ on Linux or, with the “bash-completion” Homebrew package installed on OS X, to /usr/local/etc/bash_completion.d/, respectively.

This can be done on Linux with the following Terminal commands:

sudo curl -L https://raw.githubusercontent.com/docker/docker/master/contrib/completion/bash/docker       > /etc/bash_completion.d/docker
sudo curl -L https://raw.githubusercontent.com/BioMedIA/MIRTK/master/Docker/Completion/Bash/docker-mirtk > /etc/bash_completion.d/docker-mirtk

On OS X with Homebrew, use these commands instead:

brew install bash-completion
curl -L https://raw.githubusercontent.com/docker/docker/master/contrib/completion/bash/docker        > $(brew --prefix)/etc/bash_completion.d/docker
curl -L https://raw.githubusercontent.com/BioMedIA/MIRTK/develop/Docker/Completion/Bash/docker-mirtk > $(brew --prefix)/etc/bash_completion.d/docker-mirtk

Alternatively, save the files to your home directory at, for example, $HOME/bash_completion/ and add the following lines to your .bashrc (Linux) or .bash_profile (OS X) file:

[ ! -f "$HOME/bash_completion/docker"       ] || . "$HOME/bash_completion/docker"
[ ! -f "$HOME/bash_completion/docker-mirtk" ] || . "$HOME/bash_completion/docker-mirtk"

Run the commands

The MIRTK installs a single executable named mirtk in the bin/ directory of the installation root directory. This executable is used to execute the various MIRTK commands. The name of the command must be specified as first argument of the mirtk executable. Help about a command can be printed using the special help or help-rst commands followed by the name of the command for which help is requested:

mirtk help <command>
mirtk [-v] [-v] <command> [options]

When the -v option is given to mirtk before the command name, the path and arguments of the command executable is printed before execution.

To run the commands inside a Docker container instead which does not require a local installation of MIRTK, use the following command:

docker run --rm --volume=<path>:/data biomedia/mirtk [-v] [-v] <command> [<options>]

This will download the MIRTK Docker image upon first execution. This image is stored locally and will be reused for consecutive executions. The --volume option of docker run mounts the specified directory path on the host system to the /data directory inside the MIRTK Docker container. The /data directory is the working directory of the MIRTK command. The --rm option automatically deletes the MIRTK Docker container after the command finished. Note that each docker run will create a new Docker container. As these containers are meant to be used only once for each command execution, they should be removed again after the command has finished.

For example, to print information about the NIfTI image file /path/to/my/images/image1.nii.gz using the info command, execute the Docker command:

docker run --rm --volume=/path/to/my/images:/data biomedia/mirtk info image1.nii.gz

See the Applications page for a description of each command and the available options.

Note

When Bash completion of MIRTK commands is enabled (see Bash completion), press the <tab> key twice after typing “mirtk ” or “docker run biomedia/mirtk ” (incl. a space) to see a list of all commands. To only see a list of partial matches, type “mirtk eval” or “docker run biomedia/mirtk eval”, for example, and press <tab> twice.

Write your own application

For writing your own MIRTK command or an application which uses the MIRTK libraries, we recommend a look at the source code of the applications included in the MIRTK. The API Reference generated by Doxygen provides a more detailed overview of the available MIRTK classes and their interfaces.

If you intend to contribute your applications in the future to the MIRTK distribution, see the code contribution guidelines for more information on how to contribute your code to the MIRTK source tree or develop your own MIRTK Package.