• LinuxInstall

Unpacking FreeSurfer

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.

2. cd to the directory just above where you want FreeSurfer to be installed (the ParentDir). You will need about 1G of space on this disk partition.

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'.

MINC installation

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.

• cd /usrBR mkdir -p pubsw/binBR cd pubsw/binBR ln -s which perl perlBR

2. Untar the MNI binaries and place them into the proper location. Execute the following commands:

• cd /usr/pubswBR mkdir -p packagesBR cd packagesBR tar xvfz DISTDIR/minc.tar.gz

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.