Freesurfer Uesage

VMware

Linux system: REDHAT6.5\

Freesurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

1. Initialize Freesurfer

export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

2. Basic command

recon-all -i /filepath/.nii -subject /filepath/ -all

3. Result

freeview

NOTICE: 

    Freesurfer  require good quality T1 weighted MRI data:

    (1) Resolution should be approximately 1mm³

    ^{(2) Thickness should not exceed 1.5mm (~1mm^3 is ideal)}

    ^{(According to FreeSurfer Wiki)}