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There have been various postings to the freesurfer mail list about issues running freesurfer on MacOS including M1 Macs. The information below may help with running freesurfer (Intel) binaries on MacOS including M1 Macs running BigSur (MacOS 11.6). APPLICATION SANDBOXING The privacy and security features introduced with macOS Mojave (10.14.X) and subsequently expanded in MacOS Catalina (10.15.X) and BigSur (11.X) means that after installation, binaries and applications are by default “sandboxed” and not allowed access to the disk, networked volumes, etc. - unless they are given permission. Permission should only need to be granted once, but this can be cumbersome if many binaries each need permission to run (compared to a single *.app application bundle). The System Preferences GUI can be used to grant disk access to an individual application (bundle): • Open System Preferences • Click the Security & Privacy tab • Click the Privacy tab • On the left hand side menu scroll to and select Full Disk Access • Click on the (Locked) padlock in the lower left hand corner and enter your password to unlock it • Click the + button under the list of applications in the right hand side menu; navigate using the Finder to the application you want to grant full disk access to; select it; hit the open button - OR - it may just work to directly drag the application from a Finder window into the right hand side menu • Make sure the box is checked next to the application you added • Click on the padlock icon to lock out changes The next time you launch the application, it should have full disk access. So for example you could do the above for the freeview application installed by the freesurfer 7.2.0 Mac installer package as /Applications/freesurfer/7.2.0/Freeview.app Since the binaries and scripts located under /Applications/freesurfer/7.2.0/bin are usually run from the command line using the terminal application, then one option is to grant full disk access to the terminal application. If you are comfortable with the security risk this poses, then you can use the steps above to navigate to and add /System/Applications/Utilities/Terminal.app to the list of applications with full disk access.
FREESURFER LICENSE FILE The format of older freesurfer license files may cause a runtime error, e.g., segfault on MacOS. Getting a new license file from https://secure-web.cisco.com/12l_F8Ih5rTrxaLIJ9zBhopFqvQieAKP4ZwlpWO-FYt3TT8... prevent this error. You can set the environment variable FS_LICENSE to set the path to the license file. For example, if you set that path to be $HOME/license.txt, then there is no need to use sudo/admin privileges to place a license file in an installed freesurfer distribution under /Applications. … assume you downloaded license.txt to your Downloads folder … $ cd $HOME$ pwd/Users/myuid$ cp -p -f ~/Downloads/license.txt .$ export FS_LICENSE=$HOME/license.txt <— add appropriate export to your shell init file for whatever shell you set the Terminal.app to run
MATLAB INSTALLATION ON M1 MACS The Freesurfer 7.2.0 distribution includes the script /Applications/freesurfer/7.2.0/bin/fs_install_mcr to install the Matlab R2014b run time environment. While the 7.2.0 release was built and tested with R2014b, this release is too old to be supported on M1 Macs and may cause run time errors. This will be addressed in a future freesurfer release.
RUNNING INTEL BINARIES ON M1 MACS The Freesurfer distribution is currently Intel binary only. Apple provides the built-in Rosetta2 emulation environment to translate applications built for Intel (x86_64) to run on the the M1 hardware (arm64) in real-time. Or the system detects "on the fly" if the binary is built for x86_64, and then automatically runs Rosetta2 to translate the x86_64 instructions to arm64 instructions and runs them on the M1 chip. The translation process may take longer for some binaries compared to others. On an M1 Mac, when you open the terminal window and see the shell prompt, you are by default running the arm64 version of zsh. As soon as you give a command to launch/run an Intel binary, Rosetta2 kicks in with the translation process. While existing freesurfer bash scripts should run under zsh, it is always a safe bet to run the bash shell directly (which was the default shell in older versions of MacOS), e.g, $ bashThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1TigoRcERtPmZkpJ6sxYFviEuJi8tV7Pra3nnLa084_IfzU.... … reset the SHELL environment to reflect bash ... userid@developer-Mac:~> export SHELL=/bin/bashuserid@developer-Mac:~> echo $SHELL/bin/bash If you prefer bash, it’s easier to set that as your default shell via the command line or via the GUI. See https://secure-web.cisco.com/1o3TF1SnLqZ2Nuh7KR_hCEb7CbWPiG-so7-EcBQa_435qUt...., change /bin/zsh to /bin/bash). Users who only want to run Intel binaries sometimes go a step further. Instead of running the arm64 version of “/bin/bash” (which allows for running both arm64 binaries and x86_64 binaries via Rosetta2 from the same parent shell), they instead directly run the Intel version of “/bin/bash” by invoking bash as, $ arch -x86_64 /bin/bash When running the x86_64 version of a shell then only Intel binaries can run as child processes. - R.