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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. Uncompressed (installed) size is 8.3GB. After download, you can find installation instructions for your specific platform here:

Installation instructions.

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 for Mac OS X users! Freesurfer v5.3 is NOT compatible with Apple's latest release of OSX 10.11 (El Capitan). This is because Apple's latest release implements SIP (https://support.apple.com/en-us/HT204899), a sort of security protection technology, that unfortunately breaks the way freesurfer passes library paths. We are currently making changes to the code so that freesurfer version 6.0 (when it is released) will be compliant with the new OSX changes. Until that time, you can get either download the the development version of freesurfer, or temporarily disable SIP on your El Capitan system. See the following link for instructions:

• http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/

Also, all Mac OS X platform require the installation of XQuartz for freesurfer to work properly.

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

• OSX versions 10.10 (or higher) require 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

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.

Development Version

To install the Development version of FreeSurfer, download the appropriate dev build. Some nightly dev builds are here.

Archive

Old releases 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.