7. Installation

Preparation

Please start by downloading Magia (https://github.com/tkkarjal/magia), SPM (https://www.fil.ion.ucl.ac.uk/spm/) and FreeSurfer (http://www.freesurfer.net). Install SPM and FreeSurfer according to the instructions given by the developers.

Create the necessary folders for your data using the specifications outlined in https://github.com/tkkarjal/magia/wiki/4.-Preparing-your-data-for-MAGIA.

Installing Magia

Please first add the magia-directory to your MATLAB's path: addpath('/installation/directory/magia')

Magia requires the following environmental variables in MATLAB:

• DATA_DIR: The directory where the PET data are stored under, and where Magia will operate before archiving the results
• MRI_DIR: The directory where the MRI data are stored under
• SPM_DIR: The directory where SPM is installed in
• FREESURFER_HOME: The directory where FreeSurfer has been installed in
• MAGIA_PATH: The directory where Magia has been installed in
• MAGIA_ARCHIVE: The directory under which the Magia outputs will be stored
• FS_FINAL_DIR: The directory under which the FreeSurfer results will be stored
• FS_TEMP_DIR: The directory under which FreeSurfer will operate

Please define the environmental variables in your startup.m file using setenv. If you need Magia to be available for all users of your system, you can also define the environmental variables in matlabrc.m. Please make sure the variables have been properly defined using magia_check_envs. If any of the environmental variables have not been defined, the function will throw an error message notifying about the missing environmental variable(s).

After the environmental variables have been properly specified, you are ready to start using Magia.