MacOS Install & Setup

The examples below show how to unpack/install the Freesurfer 7.0.0 beta 1 MacOS tar archive, freesurfer-darwin-macOS_HighSierra-7.0.0-beta.tar.gz, or pkg file, freesurfer-MacOS-7.0.0b1-x86_64.pkg. While the code was built and packaged on Mac OS 10.13 (High Sierra), you should follow the same instructions if you are running MacOS 10.12 (Sierra), 10.14 (Mojave) or 10.15 (Catalina).

On Mac systems, the tar archive file (.tar.gz) can be expanded under any convenient path/subdirectory on your machine you have permission to write to. For example, you can expand the tar archive under your $HOME directory. To install freesurfer under a recommended shared system location, e.g., /Applications, you may need sudo or root privileges. Please note that if you have sudo/root privileges, then you should consider using the package file (.pkg) to install the freesurfer 7.0.0 beta 1 release.

Example of placing the Mac tar archive under the $HOME directory belonging to user "tester" without using sudo/root privileges. Setup commands follow. Shell is bash or Bourne shell.

$ cd $HOME
$ pwd
/home/tester
$ tar -zxvpf freesurfer-darwin-macOS_HighSierra-7.0.0-beta.tar.gz
x freesurfer/
x freesurfer/ASegStatsLUT.txt
x freesurfer/average/
x freesurfer/bin/
x freesurfer/build-stamp.txt
x freesurfer/DefectLUT.txt
...
..
<rest of output deleted>

$ cd freesurfer
$ pwd
/home/tester/freesurfer
$ export FREESURFER_HOME=$HOME/freesurfer
$ export SUBJECTS_DIR=$FREESURFER_HOME/subjects
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-darwin-macOS_HighSierra-7.0.0-beta-xxxxxx --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/tester/freesurfer
FSFAST_HOME       /home/tester/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /home/tester/freesurfer/subjects
MNI_DIR           /home/tester/freesurfer/mni
WARNING: MINC_BIN_DIR '/home/tester/mni/bin' does not exist.
WARNING: MINC_LIB_DIR '/home/tester/freesurfer/mni/lib' does not exist.

$ which freeview
/home/tester/freesurfer/bin/freeview

Example of placing the CentOS7 tar archive under the system location /Applications by user "tester" using sudo/root privileges. Setup commands follow. Shell is bash or Bourne shell.

$ cd $HOME
$ pwd
/home/tester
$ sudo tar -C /Applications -zxvpf freesurfer-darwin-macOS_HighSierra-7.0.0-beta.tar.gz
x freesurfer/
x freesurfer/ASegStatsLUT.txt
x freesurfer/average/
x freesurfer/bin/
x freesurfer/build-stamp.txt
x freesurfer/DefectLUT.txt
...
..
<rest of output deleted>

$ export FREESURFER_HOME=/Applications/freesurfer
$ export SUBJECTS_DIR=$FREESURFER_HOME/subjects
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-darwin-macOS_HighSierra-7.0.0-beta-xxxxxx --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME       /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/subjects
MNI_DIR           /home/tester/freesurfer/mni
WARNING: MINC_BIN_DIR '/home/tester/mni/bin' does not exist.
WARNING: MINC_LIB_DIR '/home/tester/freesurfer/mni/lib' does not exist.

$ which freeview
/Applications/freeview/bin/freeview

Using the Mac Package Installer

Please note - if you already have freesurfer installed as /Applications/freesurfer, e.g., per the example above, then it is strongly advised that you remove the installation or rename the directory to be something other than freesurfer under /Applications. This is because the Mac pkg installer will install freesurfer under the path /Applications/freesurfer/<package version>.

The package installer will also save package receipts on the system and provide an uninstaller script as /Applications/freesurfer/<package version>/uninstall.sh

Performing the install

The screen shots below show the steps for running the package installer on Mac OS 10.15 (Catalina) after the security exception has been made to allow the installer to run. On older versions of Mac OS, you will not get the notifications asking if files can be read from the disk.