Neuroimaging software is not installed on the system. You must install these in your home folder. It’s easiest to just make a folder bin inside your home folder that contains all your installed software.


For standard fMRI analyses, install FSL. Download the installer script and run it to install.


Freesurfer performs anatomical and cortical surface reconstructions and segmentation. It’s a free download, from its website. you then install by

tar -xvzf Freesurfer_XXXX.tar.gz -C ~/bin/

After unpacking, it is necessary to create and copy a license file. Follow the instructions on the freesurfer website.


Follow the AFNI install instructions