FreeSurfer is a neuroimaging software package that is primarily used for processing and analysis of T1 weighted MRI. FreeSurfer is a great tool for surface-based morphometry, hippocampal and amygdala segmentations, and longitudinal analysis using linear mixed effects modelling.
The following documentation will outline FreeSurfer’s pre-processing steps, and general guidelines to analysis.
Before running anything on FreeSurfer on Artemis, you must:
load the module. e.g.
| Code Block |
|---|
module load freesurfer/7.0.1 |
2. Identify the directory in which your subject folders (in FreeSurfer format) are located
e.g. If your subjects are located in a structure that looks like this:
-scratch
-Project
-FreeSurferSubjectFolder
-subject_1
-subject_2
-subject_3
| Code Block |
|---|
export SUBJECTS_DIR=/scratch/project/FreeSurferSubjectFolder |