Freesurfer

FreeSurfer is a software package for the analysis and visualization of structural neuroimaging data.

It is developed by the Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging.

FreeSurfer provides full processing streams for structural and functional MRI and includes tools for linear and nonlinear registration, cortical and subcortical segmentation, cortical surface reconstruction, statistical analysis of group morphometry, diffusion MRI, PET analysis, and much more. It is also the structural MRI analysis software of choice for the Human Connectome Project.

For expansive documentation on using and understanding FreeSurfer tools, please visit the FS Wiki.

To run recon-all on a t1w.nii or t1w.nii.gz dataset

module load freesurfer/6.0.0
recon-all -s t1w.nii.gz -all -sd /gpfs/>path to your folder<//recon-all -s t1w.nii.gz -all -sd /gpfs/>path to your folder</

This processing takes 6-8 hours to run.

These are the output files you will see:

There is wealth of information produced here. For connectivity analysis the output in the mri folder contains the structural segmentation.

To visualize the output:

if not already: log into Oscar:

Launch the GUI via VNC session.

(if not already loaded)

module load freesurfer/6.0.0