Welcome to the templateCreator wiki!

This a wiki to introduce the templateCreator toolkit to beginners users. In summary, the templateCreator is a set of shell scripts which aims to construct DTI templates. At this moment, the templateCreator is only managing DTI images and in the future new MRI image modalities could be added. Favorite this project to your GitHub account in order yo be up-to-date with the new releases and information.

Installation Procedure

The installation procedure is pretty straightforward.

1. Download/Clone the project. I suggest downloading the most recent stable version of the code, which is regularly available in Releases packages. Pay attention to the version which you download, because some new features are maybe only available on the most recent versions.

2. Uncompress the project in the desired folder. Usually, the folder is /usr/local, but you can uncompress this package in different locations, for instance, your home directory. It is important to check if you have write permission on the folder which you want to uncompress the templateCreator compressed package.

3. Change the execute permission for all the scripts inside the templateCreator folder, located in the folder which you previously uncompressed. This procedure could be achieved with the following command line, in the terminal:

chmod u+x -R <root templateCretor folder>

This command will turn every script file inside the templateCreator folder in executable scripts, which is essential to the correct toolkit usage.

4. (Optional) Insert the templateCreator folder into the system PATH. This is a complementary step for the users which want to access the toolkit with any terminal location, i.e. you simply type the main command script and it should be accessible to any folder location. If you do not want to do this step, it is completely OK! The templateCreator scripts could be accessed normally if you previously enter the root folder before use it. First, this is the step to actually do the PATH addition:

• Check if exist a file .bashrc (or .cshrc on C-Shell systems) in your home directory. Type in the terminal which ~/.bashrc to check if this file exist. If not, you can create the file using touch ~/.bashrc After the file creation, copy and paste the following code into the .bashrc file and save it:

# templateCreator toolkit
TC_DIR=/path/to/your/templateCreator
export ${TC_DIR}
export PATH=${PATH}:${TC_DIR}:${TC_DIR}/config:${TC_DIR}/preprocessing:${TC_DIR}/posprocessing:...

Basic Usage

The main script to use is the build_template.

References

Here it is a list of scientific papers which used the templateCreator in order to build DTI specific patient/control templates.