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Description
FreeSurfer is a software package for neuroanatomical analysis of structural MRI, brain segmentation, and cortical surface reconstruction. It automatically extracts cortical thickness, subcortical structure volumes, and cortical morphology. It provides a comprehensive framework for anatomical parcellation, surface modeling, longitudinal analysis, and inter-subject registration. It constitutes an integrated implementation of numerous anatomical MRI (sMRI) methods, including automated volumetric segmentation, pial and white matter surface reconstruction, spatial normalization, cortical thickness measurement, and group-level statistical analysis.
Set up the environment
- via module
ml bio/freesurferAvailable version(s) : 8.2.0-1 (default)
- via apptainer
ml utils/apptainer
apptainer shell --bind /usr/lib64:/usr/lib64 /softs/bio/freesurfer/freesurfer-8.0.0.sif Tutorial
- Display the version of freesufer
ml bio/freesurfer
freesurfer- To launch the FreeSurfer graphical interface,
- Start an OpenOnDemand session, then start an interactive session.
- Once you are connected to the visualization server
ml utils/apptainer
apptainer exec --bind /usr/lib64:/usr/lib64 /softs/bio/freesurfer-8.0.0.sif freeview
# freeview does not work with the module bio/freesurfer