In order to install the software you should either clone this GitHub folder
git clone https://github.com/micGuerr/LongitudinalMRI.gitor Download it as a .zip file.
Next, you should add the path to the LongitudinalMRI folder. This depends on what system you are using. For bash shell the following command should work
export PATH="<path_to_folder>/LongitudinalMRI/bin:${PATH}"In order to make this changes permanent you should add the command to a bash file such as ~/.bashrc.
In order to add the path to the matlab scripts you should open matlab and type from command window:
addpath(genpath(('<path_to_folder>/LongitudinalMRI/matlab')))To make the changes permanent you should add the folder via ...
The toolbox make use of several different components which should be separately downloaded and installed:
- MRIcron (https://www.nitrc.org/projects/mricron)
- Anaconda (https://www.anaconda.com/products/individual)
- Dcm2Bids (https://github.com/UNFmontreal/Dcm2Bids)
- FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation)
- DTI-TK (http://dti-tk.sourceforge.net/pmwiki/pmwiki.php)
- FreeSurfer (https://surfer.nmr.mgh.harvard.edu/)