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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. If using the Safari web browser, a GUI is automatically opened upon completion of the download to guide the installation. If using Firefox, the .dmg file must be saved to disk first, then click on the downloaded file in Finder to launch the install. Mac OS X users may want to see how the installation will procede, described here, before beginning the download. Note: Mac OS X users must have X11 installed prior to using FreeSurfer (in Finder, look for Applications->Utilities->X11). X11 is installed via XQuartz (see Apple notes).

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).

FreeSurfer executables are available for the following platforms. Click on the filename to begin download, saving the file to your machine.

Stable 5.1 release

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

Notes:

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

• the CentOS 4 builds are known to work on CentOS 5 and 6, Ubuntu, as well as a number of other Linux variants.
• on Ubuntu, you might have to do this if qdec or freeview complain about libjpeg:

cd /usr/lib/x86_64-linux-gnu
sudo ln -s libjpeg.so.8 libjpeg.so.62

• a VMWare instance of freesurfer is not available.

• our Windows virtual machine instance is 32b, which might limit some analysis. Until a 64b instance is available, an alternative is to download the FSL 64b vm and then within that instance, download and install the 64b Centos4 x86_64 freesurfer distribution.

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 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/<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.

Ubuntu users might need to do the following in order to use the qdec app:

cd /usr/lib
ln -s libtiff.so.4 libtiff.so.3

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.