Installation

Important Note for macOS users: macOS machines require the installation of XQuartz 2.7.6.

Installing XQuartz

To see what version of macOS you have, click Apple -> About This Mac. You should see something similar to the image below:

To see what version of XQuartz you have, click Applications -> Utilities -> XQuartz. Then X11 -> About X11

If necessary, download the XQuartz installation package and double click it to install.

XQuartz 2.7.5 (macOS versions 10.6 - 10.9)
XQuartz 2.7.6 (macOS versions 10.10 and higher)

Installing FreeSurfer

Download the FreeSurfer installation package from this page. Double click the dmg then double click the freesurfer-Darwin-full.pkg to launch the installation wizard:

If you get this error:

Then you need to adjust your security settings to allow applications from 3rd party developers to be installed. To do this go to Apple -> System Preferences -> Security & Privacy -> General. Click the lock on the bottom left to make changes and under Allow applications downloaded from: select Anywhere.

After the package integrity has been verified, the introductory screen will appear. Click on Continue:

Next is the Read Me window. Click on Continue:

Next is the Software License Agreement window. Click on Continue:

Next is the Destination Select window. Click Change Install Location... to change the default installation disk and folder (/Applications/freesurfer). Or click Install to go with default:

You may need to enter you password. The installation process will begin to write files and will take a few minutes to complete.

Setup and Configuration

To begin using freesurfer, open a terminal window. The Terminal application is found under Applications -> Utilities -> Terminal:

Type the following lines in the terminal window to source the freesurfer environment:

export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

After you source freesurfer you should see some output similar to the window below:

If you use freesurfer frequently and want to avoid typing the above lines of code every time you open a terminal window, you can create a file called .profile in your home directory which contains those two line. This will cause the terminal window to automatically source freesurfer every time it is opened.

At this point you are ready to begin using the freesurfer software. If you haven't done so already, obtain a license, and copy the license.txt file into your $FREESURFER_HOME (Applications/freesurfer) directory.

Testing Freesurfer

See the this page for some example commands to test that FreeSurfer is installed and running properly.

For Mac OS systems running freesurfer 6.0.0

If you receive the following error when running the test_commands.sh.15 script:

+ cd /users/hippo/lcn/tutorial_data/tutorial_data_20190918_1558/buckner_data/tutorial_subjs/group_analysis_tutorial
+ mris_anatomical_stats -l lh.supramarg.label -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

./test_commands.sh.15: line 368: 87124 Abort trap: 6           mris_anatomical_stats -l lh.supramarg.label -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh

Then, you need to install a Freeview patch to have this work with your Mac OS version. Download the patch (~33 MB) from /autofs/cluster/pubftp/dist/freesurfer/6.0.0-patch/Freeview_6_0_0_MacOS_patch.zip follow the following instructions:

1)To download the patch, follow instructions on using the ftp file exchange from this wiki page.

2) Remove your existing Freeview.app application bundle by sending it to the trash (and then emptying the trash).You can also do this from the terminal by cd'ing to the top-level ./freesurfer subdirectory and then doing

rm -rf Freeview.app

3) Copy the new Freeview.app.zip to where your old Freeview.app was located and uncompress it (so it becomes the replacement Freeview.app in your current FreeSurfer installation).

4) Remove ./freesurfer/lib/gcc/lib/libgomp.1.dylib from your existing freesurfer installation.

5) Copy the ./freesurfer/lib/gcc/lib/libgomp.1.dylib from the patch archive to /freesurfer/lib/gcc/lib in your current freesurfer installtion.

6) Try running the Freeview.app and loading a volume with it.

-  ⇤ ← Revision 57 as of 2015-06-10 11:56:44 → 
  Size: 4064
  Editor: ZekeKaufman
  Comment:
+   ← Revision 78 as of 2020-03-04 14:59:29 → ⇥
  Size: 6456
  Editor: LeahMorgan
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 6:
-'''Before proceeding:''' Mac OSX requires the installation of XQuartz for freesurfer to function properly. OSX versions 10.6, 10.7, 10.8, and 10.9 require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]] (or earlier). OSX versions 10.10 and later require [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (or higher). Check '''Application -> Utilities''' to see if XQuartz is already installed. If not use the links to download and then install the proper version. You may need to logout and log back in after XQuartz is installed.
+'''''Important Note for macOS users:''' macOS machines require the installation of [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]].''
----
-Line 8:
+Line 9:
-{{attachment:XQuartz_screencapture.png}}
+=== Installing XQuartz ===
-Line 10:
+Line 11:
-Download the freesurfer '''dmg''' installation package and double click on it to expand the package:
+To see what version of macOS you have, click '''Apple -> About This Mac'''. You should see something similar to the image below:

{{attachment:macversion.png}}

To see what version of XQuartz you have, click '''Applications -> Utilities -> XQuartz'''. Then '''X11 -> About X11'''


{{attachment:xqfinder.png}} 
{{attachment:xqversion.png}}


If necessary, download the XQuartz installation package and double click it to install.

 * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.5.dmg|XQuartz 2.7.5]] (macOS versions 10.6 - 10.9)
 * [[http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.6.dmg|XQuartz 2.7.6]] (macOS versions 10.10 and higher)

----

=== Installing FreeSurfer ===

Download the !FreeSurfer installation package from [[DownloadAndInstall|this page]]. Double click the dmg then double click the '''freesurfer-Darwin-full.pkg''' to launch the installation wizard:
-Line 14:
+Line 36:
-## Double click on the '''mpkg''' to launch the installation wizard. If you get this error:
##
## {{attachment:install_error.png}}
## Then you need to adjust your security settings to allow applications from 3rd party developers to be installed. To do
##  ## this go to '''System Preferences -> Security & Privacy -> General'''. Click the lock on the bottom left to make ## 
## changes and under '''Allow applications downloaded from:''' select '''Anywhere'''.
## {{attachment:allow_anywhere.png}}
+If you get this error:

{{attachment:install_error.png}}

Then you need to adjust your security settings to allow applications from 3rd party developers to be installed. To do this go to '''Apple -> System Preferences -> Security & Privacy -> General'''. Click the lock on the bottom left to make changes and under '''Allow applications downloaded from:''' select '''Anywhere'''.

{{attachment:allow_anywhere.png}}
-Line 55:
+Line 78:
-export FREESURFER_HOME=/Application/freesurfer
+export FREESURFER_HOME=/Applications/freesurfer
-Line 65:
+Line 88:
-At this point you are ready to begin using the freesurfer software. If you haven't done so already, [[Registration|obtain a license]], and copy the license.txt file into your $FREESURFER_HOME (Applications/freesurfer) directory.
+At this point you are ready to begin using the freesurfer software. If you haven't done so already, [[https://surfer.nmr.mgh.harvard.edu/registration.html|obtain a license]], and copy the license.txt file into your $FREESURFER_HOME (Applications/freesurfer) directory.
-Line 71:
+Line 94:
-See the following page for some example commands to test that freesurfer is installed and running properly.
https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
+See the [[DownloadAndInstall#TestyourFreeSurferInstallation|this page]] for some example commands to test that !FreeSurfer is installed and running properly.

= For Mac OS systems running freesurfer 6.0.0 =

If you receive the following error when running the test_commands.sh.15 script:

{{{
+ cd /users/hippo/lcn/tutorial_data/tutorial_data_20190918_1558/buckner_data/tutorial_subjs/group_analysis_tutorial
+ mris_anatomical_stats -l lh.supramarg.label -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

./test_commands.sh.15: line 368: 87124 Abort trap: 6           mris_anatomical_stats -l lh.supramarg.label -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh
}}}

Then, you need to install a Freeview patch to have this work with your Mac OS version. Download the patch (~33 MB) from /autofs/cluster/pubftp/dist/freesurfer/6.0.0-patch/Freeview_6_0_0_MacOS_patch.zip follow the following instructions:

1)To download the patch, follow instructions on using the ftp file exchange from [[https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange|this]] wiki page.

2) Remove your existing Freeview.app application bundle by sending it to the trash (and then emptying the trash).You can also do this from the terminal by cd'ing to the top-level ./freesurfer subdirectory and then doing
{{{
rm -rf Freeview.app
}}}

3) Copy the new Freeview.app.zip to where your old Freeview.app was located and uncompress it (so it becomes the replacement Freeview.app in your current FreeSurfer installation).

4) Remove ./freesurfer/lib/gcc/lib/libgomp.1.dylib from your existing freesurfer installation.

5) Copy the ./freesurfer/lib/gcc/lib/libgomp.1.dylib from the patch archive to /freesurfer/lib/gcc/lib in your current freesurfer installtion.

6) Try running the Freeview.app and loading a volume with it.