
FreeSurfer is an open source software suite for processing and analyzing (human) brain MRI images.
- Skullstripping
- Image Registration
- Subcortical Segmentation
- Cortical Surface Reconstruction
- Cortical Segmentation
- Cortical Thickness Estimation
- Longitudinal Processing
- fMRI Analysis
- Tractography
- FreeView Visualization GUI
- and much more..
The freesurfer downloads can be found here
The Tar GZ for Linux Install can be found here
% tar -zxvpf freesurfer-linux-centos7_x86_64-7.0.0.tar.gz
% cd freesurfer
Prepare the Environment in your .bashrc
export FREESURFER_HOME=/usr/local/freesurfer
export FSFAST_HOME=$FREESURFER_HOME/fsfast
export FSF_OUTPUT_FORMAT=nii.gz
export FMRI_ANALYSIS_DIR=$FREESURFER_HOME/fsfast
export FUNCTIONALS_DIR=$FREESURFER_HOME/sessions
export FS_OVERRIDE=0
export MNI_DIR=$FREESURFER_HOME/mni
export MINC_BIN_DIR=$FREESURFER_HOME/mni/bin
export MINC_LIB_DIR=$FREESURFER_HOME/mni/lib
export MNI_DATAPATH=$FREESURFER_HOME/mni/data
export PERL5LIB=$FREESURFER_HOME/mni/share/perl5
export MNI_PERL5LIB=$FREESURFER_HOME/mni/share/perl5