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FreeSurfer is a free software suite for preprocessing and analyzing anatomical MRI data. The lab primarily uses FreeSurfer for reconstructing and segmenting anatomical images. The FreeSurfer wiki has extensive documentation describing FreeSurfer functions as well as useful tutorials and troubleshooting information (for example for the highly used recon-all function).

  1. To download FreeSurfer go to this page.
  2. To set up FreeSurfer for MacOS you can refer to this page.
    and follow our lab-specific setup:

     Click here for our lab specific setup

    We use version 6.0 (latest stable version as of 2018/08/15, size = 4.4 GB).

    The FreeSurfer setup in the bash profile contains one extra line to indicate the directory with subject data:

    Bash Setup
    ## Open the bash profile
    open ~/.bash_profile
    ## Add the following lines:
    # Freesurfer Setup
    export FREESURFER_HOME=/Applications/freesurfer
    source $FREESURFER_HOME/
    export SUBJECTS_DIR=/Volumes/server/Freesurfer_subjects


    (Optional for Matlab users) You can allow Matlab to access FreeSurfer functions by editing your startup.m and add the following lines:

    MATLAB Setup
    fshome = getenv('FREESURFER_HOME');
    fsmatlab = sprintf('%s/matlab',fshome);		
    if (exist(fsmatlab) == 7)
    clear fshome fsmatlab;
    fsfasthome = getenv('FSFAST_HOME');
    fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
    if (exist(fsfasttoolbox) == 7)
    clear fsfasthome fsfasttoolbox
  3. After installing, you need to obtain a license and copy the license.txt file into your $FREESURFER_HOME directory (e.g., /Applications/freesurfer). For instructions see this page).
    Most likely, you can’t save the license file directly into your FreeSurfer folder. If that is the case, save the license.txt file somewhere else and then copy it to the FreeSurfer folder by typing in the Terminal:

    Copy FreeSurfer license
    sudo cp PATH_TO_LICENSE/license.txt /Applications/freesurfer
  4. You can check if your installation was successful by following these examples.






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