INSTALL file for FreeSurfer distribution
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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.
Instructions for updating an existing installation are at FreeSurferUpdate.
The distribution consists of the following files which can either be downloaded from http://surfer.nmr.mgh.harvard.edu or obtained from a CDROM.
If you downloaded the distribution, unpack the tarball with this command:
tar zxvf <the-file-you-downloaded>
This will create a directory called freesurfer, which will henceforth be referred to as DISTDIR.
If you are getting the files from a CDROM, the top level of the CDROM should have the following files in it. Use this directory as DISTDIR.
In DISTDIR are the following files:
INSTALL -- this file BR license.freesurfer -- license agreement BR freesurfer.tar.gz -- FreeSurfer treeBR talairach.tar.gz -- MNI 305 talairach brainBR minc.tar.gz -- MNI MINC tools/binariesBR bert.raw.tar.gz -- FreeSurfer tutorial dataBR bert.func.tar.gz -- FreeSurfer functional tutorial dataBR bert.recon.tar.gz -- reconstructed FreeSurfer tutorial dataBR average7.tar.gz -- contains average labels for checking spherical morphBR
To install FreeSurfer from tar files
1. Obtain a license key from http://surfer.nmr.mgh.harvard.edu/download.html or from a previous installation. If you are using a previous installation, the license file should be freesurfer/.license.
3. Enter the command:
tar xvfz DISTDIR/freesurfer.tar.gz
This will create a directory called freesurfer.
4. The default subjects directory (the directory in which your subjects' data will be placed) is freesurfer/subjects. You may wish set to up your installation differently, e.g. if you have a large external hard drive you want to use for subject data. See below for details. Regardless, cd into your subjects directory and enter the commands:
tar xvfz DISTDIR/average7.tar.gz BR tar xvfz DISTDIR/bert.recon.tar.gz
This will populate your subjects directory with 'average7', and the FS tutorial's sample data set 'bert'.
FreeSurfer uses some of the tools developed at the Montreal Neurological Institue (MNI) (http://www.bic.mni.mcgill.ca) to align antomical volumes (using minctracc) and to compute the Talairach transform (using mritotal). You must have the MNI tools installed to be able to access this functionality through FreeSurfer.
The tools can be downloaded and installed directly from the MNI. As a service to our users, we also offer binaries for the MNI tools. Unfortunately, once the MNI binaries have been created, they will not work unless they are located in the same directory where they were compiled. Accordingly, if you want to install the binaries we supply, you will have to put them in the same place we put them. Also, perl must be in the same place as on our system.
To install our binaries
1. Create a symbolic link to your perl in the location that matches ours. Execute the following commands. Note that you may need to execute some of them with root permission; su to root, use sudo, or talk to your system administrator.
2. Untar the MNI binaries and place them into the proper location. Execute the following commands:
Install MNI talairach subject
Those not using the functional stream can skip this step.
1. cd to your subjects directory and enter the following command:
tar xvfz DISTDIR/talairach.tar.gz
This will create a directory called talairach.
To configure FreeSurfer
1. Copy the license file into freesurfer/ and rename it to ".license" (no quotes) if necessary.
2. The file freesurfer/FreeSurferEnv.csh is a csh (c-shell) script that will configure your environment so that you can use FreeSurfer. It sets a few envrionment variables and performs some sanity checks. If you are comfortable writing shell scripts, you may wish to set up your system differently, but we recommend the following:
Create a file in your home directory called something like "SetUpFreeSurfer.csh" with the following contents:
# Additional configurations will go here.BR
The full path to your freesurfer directory should be something like:
2. If you wish to designate a non-default subjects directory, add the following line in the 'additional configurations' section, before 'cd $FREESURFER_HOME' is called:
setenv SUBJECTS_DIR <full path to subject dir>
3. If you installed the MINC tools, then add the following lines to the additional configuration section:
setenv MINC_BIN_DIR /usr/pubsw/packages/mni/current/binBR setenv MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib
If you did not install the MINC tools, then add the following line in the local setup section:
4. If you do NOT intend to use the functional tools, then add the following line to the additional configuration section:
If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file:
5. Save the file. You will need to source this file every time you want to use Freesurfer.
6. Make sure you are using csh or tcsh. You can check by typing 'ps' at the command line. If you do not see csh or tcsh as one of the processes in the right hand column of output, you must change your default shell to csh or tcsh or explicitly launch csh or tcsh first.
To explicitly launch csh or tcsh (tcsh is recommended), simply enter the following command:
You may notice your prompt change. Note that some of your login files may not be run in the new shell environment. See the man pages for tcsh for details.
7. Source the script.
You should see output like this:
Setting up enviroment for FreeSurfer/FS-FASTBR FREESURFER_HOME /home/freesurferBR FSFAST_HOME /home/freesurfer/fsfastBR AFNI_DIR /home/freesurfer/afniBR FSL_DIR /home/freesurfer/fslBR SUBJECTS_DIR /home/freesurfer/subjectsBR
If you see any warnings, you can probably safely ignore them, but make sure they are not notifying you that it can't find something you think should exist.
If you see any error messages, make sure you have performed the installation process properly, and that your FREESURFER_HOME setting is correct.
From now on, you only need to source the SetUpFreeSurfer.csh script once in a shell session to be able to run FreeSurfer. You may want to do this in our shell's login scripts (i.e. .cshrc or .tcshrc).
To use FreeSurfer
See $FREESURFER_HOME/docs/FreeSurferManual.pdf to get started. See also http://surfer.nmr.mgh.harvard.edu/docs/ 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:
libtiff BR dlcompat-dev
FTP File Exchange
Use ftp surfer.nmr.mgh.harvard.edu. Login as anonymous and password as "email-address".
ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (184.108.40.206). 220 surfer.nmr.mgh.harvard.edu FTP server (Version wu-2.6.2-11.73.1) ready. Name (surfer.nmr.mgh.harvard.edu:tosa): anonymous 331 Guest login ok, send your complete e-mail address as password. 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.