FreeSurfer

Freesurfer is not supported on Ubuntu 24, which is the OS on the SPICE. However, it is possible to run FreeSurfer using a Singularity container. The fMRIPrep container has all the needed dependencies.

Run the following command from the terminal to start it.

singularity shell --bind $(pwd):$(pwd) --cleanenv /scratch/singularityContainers/fmriprep.simg

You need a freesurfer license. If you don't have one, follow this link. Upload it to SPICE and define the path to the FS_LICENSE in the singularity terminal.

export FS_LICENSE=<path_to_freesurfer_license>

Next step is to define the freesurfer SUBJECTS_DIR where the output will be saved to.

SUBJECTS_DIR="<path_to_SUBJECTS_DIR>"

Now you are ready to run freesurfer!

recon-all -subject <subject id> -i <path_to_t1> -all