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FreeSurfer Installation

Linux Installation


Mac OS X Installation




INSTALL file for FreeSurfer distribution

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FreeSurfer is copyright (c) CorTechs, 1999. All rights reserved.

FreeSurfer is being distributed with executables for Linux/Intel, Darwin/Mac OS X, and SunOS. This is an alpha release and has not been extensively tested. The software is offered "as is" without any guarantees and should not be used for clinical applications. See license.freesurfer for additional restrictions. See docs/license.afni for restrictions on and citations for the use of the AFNI software package and how to cite it. See docs/license.minc for restrictions on and citations for the use of the MINC software package.

Note: These instructions are for installing a new distribution of FreeSurfer. If you want to update an existing FreeSurfer distribution, you should download the snapshot update version from:

Instructions for updating an existing installation are at FreeSurferUpdate.

To use FreeSurfer

See $FREESURFER_HOME/docs/FreeSurferManual.pdf to get started. See also See also recon-all -help

Mac OS X Notes

1. You may need to use the OS X minc 1.2 available from the MNI website. There are bugs in it, but MNI has promised a fix soon.

2. You should use fink to install the additional libraries that FreeSurfer needs, such as libtiff and libdl. You can get fink from:

Once you've installed fink, there are two packages you'll need to install:

FTP File Exchange

Use ftp Login as anonymous and password as "email-address".

Connected to (
220 FTP server (Version wu-2.6.2-11.73.1) ready.
Name ( anonymous
331 Guest login ok, send your complete e-mail address as password.
230 Guest login ok, access restrictions apply.
Remote system type is UNIX.
Using binary mode to transfer files.

If you are getting files, then 

   ftp> cd transfer/outgoing

If you are putting files, then

   ftp> cd transfer/incoming

Then go to a particular directory.

For those inside NMR center, go to /space/outgoing and put files in its subdirectory. You can get user transfered files from /space/incoming. It takes 5 minutes or so to actually see the files there after the transfer.