top | previous | next

FreeSurfer Download

FreeSurfer for Linux is distributed in the form of a .tar.gz file, and is installed from the terminal command-line. The Mac OS X FreeSurfer distribution is a .dmg file. Uncompressed (installed) size is 8.3GB. After download, you can find installation instructions for your specific platform here:

Installation instructions.

Important Note! When processing a group of subjects for your study, it is essential to process all your subjects with the same version of freesurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms (for instance the 32b and 64b CentOS 4 builds should produce identical results), there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions).

Important Note! On Mac OS X platforms, you need to install XQuartz for freesurfer to work properly.

• OSX versions 10.6, 10.7, 10.8 and 10.9 require XQuartz 2.7.5.

• OSX version 10.10 requires XQuartz 2.7.6 or higher.

Freesurfer 5.3 stable release

Please refer to the ReleaseNotes page for per-release information.

FAQ:

• Virtualbox installation instructions can be found here.

  • the root password for the Virtualbox release is freesurfer

• here is the md5sum data and sha1sum data for confirming tarball integrity after download.

• on Ubuntu, you might have to do this if qdec or freeview complain about libjpeg or libtiff:

cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros)
sudo ln -s libjpeg.so.8 libjpeg.so.62
sudo ln -s libtiff.so.4 libtiff.so.3

Freeview dev version

Below are the links to the daily builds of the Freeview imaging software. Please be aware that daily builds of Freeview will contain the most up-to-date features, but will also possibly contain bugs or other undesirable behavior because daily builds have not had adequate time to be rigorously tested.

Instructions:

• For Linux systems, download the file and copy it over the existing $FREESURFER_HOME/bin/freeview.bin file.

• For Mac OSX systems:

  1. Use the above link to download the new Freeview bundle, then double click to unzip it.

  2. Delete the existing Freeview bundle from your $FREESURFER_HOME directory.

  3. Drag the new Freeview bundle into your $FREESURFER_HOME directory.

     • On most OS X systems FREESURFER_HOME = /Applications/freesurfer

wget

If you are having problems downloading the installation from your browser, you could use the command-line 'wget' utility ('curl -O' on the Mac):

wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/<filename>

where <filename> is a filename from the Download column in the table above. Note that the '-c' flag allows continuing a failed partial download.

Archive

Old releases are here.

Dev

Some nightly dev builds are here.

Notes

uname -m

If the output says 'x86_64', you have a 64-bit Intel-compatible machine.

Note that a license key file is necessary to run the FreeSurfer binaries (but is not necessary to download and install FreeSurfer).

Registration is here.

Upon completion of the download, proceed to the installation section.

iSurf App

A brain segmentation tutorial application for the iPhone/iPad created by an external developer, making use of Freesurfer's segmentation, is available here.