Day: September 8, 2021

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Setting up FreeSurfer 7.2.0 for CentOS-7

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