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| This page takes you through all the steps necessary for downloading & installing !FreeSurfer but lacks the detail and options presented throughout the DownloadAndInstall wiki. |
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| RAM: 4GB at least (8GB recommended)<<BR>> Graphics card: 3D with its own graphics memory & accelerated OpenGL drivers<<BR>> Install's Disk space usage: 8.5GB<<BR>> Typical subject size: 370MB<<BR>> |
RAM: 8GB recommended<<BR>> Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers<<BR>> Size of installation package: 8.5GB<<BR>> Typical size of a processed subject: 370MB<<BR>> |
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| Other requirements: Matlab (to run FS-FAST) | Other requirements: Matlab (only needed to run FS-FAST, the fMRI analysis stream) |
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| '''Important:''' It is essential to process all your subjects with the same version of !FreeSurfer, on the same OS platform and vendor, and to be completely safe, even the same version of the OS. | '''Freesurfer 5.3 stable release''' (ReleaseNotes) |
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| == Freesurfer 5.3 stable release == Please refer to the ReleaseNotes page for per-release information. |
'''Important Note:''' It is essential to process all your subjects with the same version of !FreeSurfer, on the same OS platform and vendor, and to be completely safe, even the same version of the OS. |
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| '''Development Version:''' <<BR>>The most recent build of !FreeSurfer can be download from [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev|here]]. |
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| Please select the instructions for the type you downloaded (and be sure to come back to this page afterwards): * [[LinuxInstall|Linux Installation]] |
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| * [[MacOsInstall|Mac OS X Installation]] | '''Linux:''' |
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| * [[Installation/FreeSurferVirtualImage|FreeSurfer Virtual Image Installation using VirtualBox]] | Installing freesurfer on Linux systems involves simply extracting the contents of the .tar.gz file somewhere on your machine. Installing into the directory {{{/usr/local}}} is recommended. For example: {{{ $> tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz }}} '''Mac:''' Installing freesurfer on Mac systems involves simply double clicking the .dmg file and clicking thru the steps. The default installation location is in the {{{/Applications}}} directory. For more detailed instructions, please see the following [[MacOsInstall#SetupandConfiguration|step-by-step]]. == Setup & Configuration == To begin using !FreeSurfer, you must define and evironment variable called '''{{{FREESURFER_HOME}}}''' which is set to the location !FreeSurfer was installed, and then source the setup script: '''Linux:''' {{{ ## bash $> export FREESURFER_HOME=/usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh ## tcsh $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh }}} '''Mac:''' {{{ export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh }}} Is done correctly, you should see output similar to this: {{{ Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni }}} == License == A license key must be obtained to make the !FreeSurfer tools operational. Obtaining a license is free and comes in the form of a license.txt file. Once you obtain the license.txt key file, copy it to your !FreeSurfer installation directory. This is also the location defined by the '''{{{FREESURFER_HOME}}}''' environment variable. [[https://surfer.nmr.mgh.harvard.edu/registration.html|Follow this link to obtain a license key.]] == Test your FreeSurfer Installation == Close any terminal windows you have open and then open a new one. Copy and paste this command into the terminal window: {{{ freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz \ -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow \ -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow \ -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red \ -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red }}} The above command will open the freeview GUI and the subject named 'bert' which comes with your !FreeSurfer installation and can be used as an example for what !FreeSurfer output should look like. == Sign up for the Mailing List == If you encounter problems with your installation or have any questions about !FreeSurfer, you can |
This page takes you through all the steps necessary for downloading & installing FreeSurfer but lacks the detail and options presented throughout the DownloadAndInstall wiki.
Contents
FreeSurfer System Requirements
Summary of Requirements:
Operating System: Linux, Mac OS X, Windows (via VirtualBox)
Processor Speed: 2GHz at least
RAM: 8GB recommended
Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers
Size of installation package: 8.5GB
Typical size of a processed subject: 370MB
Tutorial dataset size: 18GB
Other requirements: Matlab (only needed to run FS-FAST, the fMRI analysis stream)
Download
Freesurfer 5.3 stable release (ReleaseNotes)
Important Note: It is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and to be completely safe, even the same version of the OS.
OS |
Platform |
Version |
Release Date |
Download |
Size |
Linux |
CentOS 6 x86_64 (64b) |
stable v5.3.0 |
15 May 2013 |
4.2G |
|
Linux |
CentOS 4 x86_64 (64b) |
stable v5.3.0 |
15 May 2013 |
4.0G |
|
Linux |
CentOS 4 (32b) |
stable v5.3.0 |
15 May 2013 |
3.8G |
|
Mac |
Lion OX X 10.7 (64b Intel) |
stable v5.3.0 |
15 May 2013 |
3.5G |
|
Mac |
SnowLeopard OS X 10.6 (32b Intel) |
stable v5.3.0 |
15 May 2013 |
3.2G |
|
Virtualbox |
Xubuntu 12.04 |
stable v5.3.0 |
15 Aug 2013 |
9.0G |
Development Version:
The most recent build of FreeSurfer can be download from here.
Installation
Linux:
Installing freesurfer on Linux systems involves simply extracting the contents of the .tar.gz file somewhere on your machine. Installing into the directory /usr/local is recommended. For example:
$> tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
Mac:
Installing freesurfer on Mac systems involves simply double clicking the .dmg file and clicking thru the steps. The default installation location is in the /Applications directory. For more detailed instructions, please see the following step-by-step.
Setup & Configuration
To begin using FreeSurfer, you must define and evironment variable called FREESURFER_HOME which is set to the location FreeSurfer was installed, and then source the setup script:
Linux:
## bash $> export FREESURFER_HOME=/usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh ## tcsh $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh
Mac:
export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh
Is done correctly, you should see output similar to this:
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni
License
A license key must be obtained to make the FreeSurfer tools operational. Obtaining a license is free and comes in the form of a license.txt file. Once you obtain the license.txt key file, copy it to your FreeSurfer installation directory. This is also the location defined by the FREESURFER_HOME environment variable.
Follow this link to obtain a license key.
Test your FreeSurfer Installation
Close any terminal windows you have open and then open a new one.
Copy and paste this command into the terminal window:
freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz \ -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow \ -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow \ -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red \ -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
The above command will open the freeview GUI and the subject named 'bert' which comes with your FreeSurfer installation and can be used as an example for what FreeSurfer output should look like.
Sign up for the Mailing List
If you encounter problems with your installation or have any questions about FreeSurfer, you can