Using FreeSurfer on the SCC

Loading the FreeSurfer Module

The SCC uses a module system to load and access software packages. Refer to our module page for more extensive documentation.

To see all versions of FreeSurfer availble on the SCC, you can search for the package with the module command:

[scc4]$ module avail freesurfer

To list available version of FreeSurfer in a different manner:

[scc4]$ module spider freesurfer

To load the a specific version of FreeSurfer (7.3.2):

[scc4]$ module load freesurfer/7.3.2

-------- freesurfer-linux-centos7_x86_64-7.3..2-20220717-7725d89 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /share/pkg.7/freesurfer/7.3.2/install
FSFAST_HOME       /share/pkg.7/freesurfer/7.3.2/install/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /share/pkg.7/freesurfer/7.3.2/install/subjects
TUTORIAL_DATA     /share/pkg/freesurfer/7.3.2/install/subjects/tutorial_data/buckner_data/tutorial_subjects
MNI_DIR           /share/pkg.7/freesurfer/7.3.2/install/mni

Succesfully loading FreeSurfer will return the above path definitions. Note the SUBJECTS_DIR variable, as this is the path that you will reassign to where your subject data is.

AlmaLinux 8 Transition

Refer to our AlmaLinux8 page for more extensive documentation.

Consistency testing has been conducted and the results are summarized in the table below. It's recommended to use our singularity container for CentOS7 if you need to use Freesurfer/5.3.0.

FreeSurfer Version	Results	Must Use Container
5.3.0	different	yes
2019-08-12_dev	different	yes
6.0	same	no
7.1.0	same	no
7.2.0	same	no
7.3	same	no
7.3.2	same	no
7.4.1	NEW on Alma8	no