FreeSurfer v6.0 (beta release)

The FreeSurfer development team seeks beta testers for the beta version of FreeSurfer v6.0. This is a beta release to the FreeSurfer community to help identify bug fixes and other unknown issues before the stable release of FreeSurfer v6.0. We ask beta testers to submit any problems or issues they may encounter to the freesurfer support list. And follow our protocols for submitting a bug report. It would also be helpful to know if the issue you encounter exists in v5.3 as well.

PLEASE REMEMBER THAT THIS IS NOT AN "OFFICIAL" RELEASE AND CHANGES MAY BE MADE THAT WOULD REQUIRE THAT YOU REANALYZE YOUR DATA.

We anticipate an approximately 2 week beta testing period.

FreeSurfer System Requirements

Summary of Requirements:
Operating System: Linux, Mac OS X
Processor Speed: 2GHz at least
RAM: 8GB recommended
Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers
Size of installation package: 10GB
Typical size of a processed subject: 300MB
Other requirements: Matlab (only needed to run FS-FAST, the fMRI analysis stream)

Download

FreeSurfer 6.0-beta ReleaseNotes

Important Note for Mac OS X users: Mac OS X platform requires the installation of XQuartz 2.7.6 for FreeSurfer to work properly.

Installation

Installing FreeSurfer involves simply extracting the contents of the .tar.gz file somewhere on your machine. Installing into the directory /usr/local is recommended. For example:

$> tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161028-4cfbf2a.tar.gz

Setup & Configuration

To begin using FreeSurfer, you need to open a terminal window and define and environment variable called FREESURFER_HOME which is set to the location FreeSurfer was installed, and then source the setup script. Sourcing FreeSurfer needs to be done every time you open a new terminal window. Or, you can add the two lines below to your default setup file (.bashrc or .cshrc) and FreeSurfer will be sourced automatically everytime you open a new window.

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

## tcsh
$> setenv FREESURFER_HOME /usr/local/freesurfer
$> source $FREESURFER_HOME/SetUpFreeSurfer.csh

If done correctly, you should see output similar to this:

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME     /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR    /usr/local/freesurfer/subjects
MNI_DIR         /usr/local/freesurfer/mni

License

A license key must be obtained to make the FreeSurfer tools operational. Obtaining a license is free and comes in the form of a license.txt file. Once you obtain the license.txt key file, copy it to your FreeSurfer installation directory. This is also the location defined by the FREESURFER_HOME environment variable.

Follow this link to obtain a license key.

Test your FreeSurfer Installation

FreeSurfer comes with two sample data files (sample-001.mgz and sample-002.mgz) as well as a fully recon-ed subject named bert. These data files can be used to test that your FreeSurfer installation was done properly. To test your installation, please try the following examples:

Example 1: Convert the sample-001.mgz to nifti format.

$> cd $FREESURFER_HOME/subjects
$> mri_convert sample-001.mgz sample-001.nii.gz
...
reading from sample-001.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to sample-001.nii.gz...

Example 2: View the output volumes, surfaces and subcortical segmentation of fully recon-ed subject bert.

$> cd $FREESURFER_HOME/subjects
$> freeview -v \
    bert/mri/T1.mgz \
    bert/mri/wm.mgz \
    bert/mri/brainmask.mgz \
    bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
    -f \
    bert/surf/lh.white:edgecolor=blue \
    bert/surf/lh.pial:edgecolor=red \
    bert/surf/rh.white:edgecolor=blue \
    bert/surf/rh.pial:edgecolor=red

The freeview above command will open the freeview GUI and should look similar to the image below.