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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. | ## page was renamed from QuickInstall = FreeSurfer Download and Install = == Internal FreeSurfer == People within the [[MartinosCenter|MGH/MIT/HMS Martinos Center]] should use the [[InternalFreeSurferDistributions|InternalFreeSurferDistributions]]. Freesurfer is already installed on your system. |
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| '''Important Note for Mac OS X users:''' Mac OS X platform requires the installation of XQuartz for freesurfer to work properly. Pre-Yosemite versions of OSX require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]]. Post-Yosemite versions of OSX require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (or higher). |
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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]]. |
'''Development Version:''' Daily builds of !FreeSurfer can be downloaded from [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev|here]]. '''Previous Releases:''' Old releases of !FreeSurfer can be downloaded from [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer|here]]. |
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| '''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: |
'''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: |
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| '''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]]. |
'''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]]. |
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| 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: | To begin using !FreeSurfer, you need to open a terminal window and define and environment variable called '''{{{FREESURFER_HOME}}}''' which is set to the location !FreeSurfer was installed, and then source the setup script. Sourcing !FreeSurfer needs to be done every time you open a new terminal window. Or, you can add the two lines below to your default setup file (.bashrc or .cshrc) and !FreeSurfer will be sourced automatically everytime you open a new window. |
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| export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh |
$> export FREESURFER_HOME=/Applications/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.sh |
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| Is done correctly, you should see output similar to this: | If done correctly, you should see output similar to this: |
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| Close any terminal windows you have open and then open a new one. | !FreeSurfer comes with two sample data files (sample-001.mgz and sample-002.mgz) as well as a fully recon-ed subject named bert. These data files can be used to test that your !FreeSurfer installation was done properly. To test your installation, please try the following examples: |
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| Copy and paste this command into the terminal window: | '''Example 1:''' Convert the sample-001.mgz to nifti format. |
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| 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 |
$> cd $FREESURFER_HOME/subjects $> mri_convert sample-001.mgz sample-001.nii.gz ... reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... |
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| 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. | '''Example 2:''' View the output volumes, surfaces and subcortical segmentation of fully recon-ed subject bert. {{{ $> cd $FREESURFER_HOME/subjects $> freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red }}} |
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| == Sign up for the Mailing List == If you encounter problems with your installation or have any questions about !FreeSurfer, you can |
The freeview above command will open the freeview GUI and should look similar to the image below. {{attachment:freeview_67.jpeg}} == Additional Resources == [[https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials|Try our tutorials]] [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription|Sign up for a FreeSurfer course]] [[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport|Join the FreeSurfer mailing list, ask a question, or view the archives]] |
FreeSurfer Download and Install
Internal FreeSurfer
People within the MGH/MIT/HMS Martinos Center should use the InternalFreeSurferDistributions. Freesurfer is already installed on your system.
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.
Important Note for Mac OS X users: Mac OS X platform requires the installation of XQuartz for freesurfer to work properly. Pre-Yosemite versions of OSX require XQuartz 2.7.5. Post-Yosemite versions of OSX require XQuartz 2.7.6 (or higher).
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: Daily builds of FreeSurfer can be downloaded from here.
Previous Releases: Old releases of FreeSurfer can be downloaded 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 need to open a terminal window and define and environment variable called FREESURFER_HOME which is set to the location FreeSurfer was installed, and then source the setup script. Sourcing FreeSurfer needs to be done every time you open a new terminal window. Or, you can add the two lines below to your default setup file (.bashrc or .cshrc) and FreeSurfer will be sourced automatically everytime you open a new window.
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
If 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
FreeSurfer comes with two sample data files (sample-001.mgz and sample-002.mgz) as well as a fully recon-ed subject named bert. These data files can be used to test that your FreeSurfer installation was done properly. To test your installation, please try the following examples:
Example 1: Convert the sample-001.mgz to nifti format.
$> cd $FREESURFER_HOME/subjects $> mri_convert sample-001.mgz sample-001.nii.gz ... reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz...
Example 2: View the output volumes, surfaces and subcortical segmentation of fully recon-ed subject bert.
$> cd $FREESURFER_HOME/subjects
$> freeview -v \
bert/mri/T1.mgz \
bert/mri/wm.mgz \
bert/mri/brainmask.mgz \
bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f \
bert/surf/lh.white:edgecolor=blue \
bert/surf/lh.pial:edgecolor=red \
bert/surf/rh.white:edgecolor=blue \
bert/surf/rh.pial:edgecolor=redThe freeview above command will open the freeview GUI and should look similar to the image below.
Additional Resources
Sign up for a FreeSurfer course
Join the FreeSurfer mailing list, ask a question, or view the archives