External Email - Use Caution Thank you! It worked. FYI I've installed 7.1.
best, Elmira On Sat, Oct 2, 2021 at 9:37 PM fsbuild <fsbu...@contbay.com> wrote: > Hello Elmira, > > You could try what’s listed in this posting to the freesurfer mailing > list, > https://secure-web.cisco.com/14r6HUNpUdecs2uurR0aVhufM6oEIRKkatZhBvFY94EHiSZYqp8rG1482Iq2VG9TDvSgmhdPI1A3mb6jQ5iMrH4uesSDg5ZyAdavkcIWS4iw_mJ6JmfVPiaHSEEk1mBQhrEF6FvzA9N-8dUWNEyV3E1CP0p19IoLSnhCxwBWBeZfU3-E-s0N8IfW0BXprbyISf28zfCY4kRCp4NOk5UOU3rRsYIcKp1sHhvGsMBIN3xDeaZcbGGwhmNTRm1xI_kCNSM8MkkOK79oB4mPaSoHXJg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmaillist.html, > from last month, > https://secure-web.cisco.com/1bN_QoWv7_mMLp3fX8AvqovcSiCmF8fy0bMu4OTkZeJVFcnwvgw3KZ4m6xPb_JHqcgxPjC3oyIIwd3d3bU51P8pFY4YhFuPJevhysEsnWaoIUjkplJZxidW7uMg2C_tdOLioNRQ_YOBrNjU_NteQirOLCWy1ronwWWN132uZaVONadSi8vXDQNePu4WTfWPOUiOyg-WVr5D4RqLYRxyzrx40bHmxcEGlajODxMUk7Fi0Gjz33pM_YvekPiEQCabN2D2EM8Z8nzfpv5tOWXvDkfw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg70979.html. > I’ve copied it below as well. > > I can’t see from your crash report if you installed the latest 7.2.0 > release (via the installer > https://secure-web.cisco.com/12v10hIiR8nFLjoZsoRpIYYuNSPeaYf-J6Yf7a5CztS85LQEGLq2vO4YjNYX-PkIAP6tsL6hLUp7k3EbCXRJzavBca9iI6QU3Gi2WsXGF5EPtJJZSsaD5RnEpXhp55-DXuWUeP1-od7zbSRj8Oh3ywhkEqHWCE9023KgtIJn8cVi-Le4mCgxON90LY7hjuTNquiFe0LySRHLF1AVTWlX6XLBW9XTrmhw5PoGX4qN3aSUD3bnYC8PNldAGhAXhxOkwHcDa05jbB67iNQfFk7Aw7g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7..2.0%2Ffreesurfer-darwin-macOS-7.2.0.pkg_ > <https://secure-web.cisco.com/1PlUHT0NhEO_c102zjohFCD3-mQQoJ9N_RJes2fcWJvHJYaU0nIgfs0XckqDAC6irGQ5NnrkGqTTKNQn0khNvaK5gDEmhVPxAiZ55MY6XU00PNvrQHr4ZHHLO7r3cFRr2ejZOaTZ3hKgFXu4xf92Q9v7kkleA6dj5Tbu2K5IPS7rPzwjvtKUPL5-P7s_YUdzpWk_dVjhKth4rzL84LgvJKVJOuf9HXu8Ic-1qvi8Ns5RhtVLaHe5UQNA_CHJvVk2bIQpYUqKaoBja6zgmSYK9cg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-darwin-macOS-7.2.0.pkg_> > ). But if you are not running the latest release, then I would also give > that a try. > > - R. > > On Oct 2, 2021, at 20:35, Elmira Hassanzadeh <elm...@gmail.com> wrote: > Hello FreeSurfer Developers, > > I installed freesurfer for the first time on my system but although the > installation went smoothly I cannot open freeview. Here is the error I > receive on terminal (the full log at the end of this message) > > 9800 Segmentation fault: > 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" > > > > Begin forwarded message: > > *Subject: **[Freesurfer] Notes on running freesurfer on MacOS (including > M1 Macs running MacOS BigSur 11.6)* > *Date: *September 22, 2021 at 21:15:35 EDT > *To: *freesurfer@nmr.mgh.harvard.edu > > 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/1QMftmSEkoOcMup8n7cdsjGsnt_jh6CcognWlaFpWHLJcs7auJEDBbMJbLRezgiT8UF54ERqSEfWuxhrcKwFcqqNhjMAsmIWiLd2UoPF0seMKkt6Wc0rvdZlYHI6pv0bq7IRXU3xbUXPr4Unz9UigY6jNqDUTsPBnO_8ENIoreFxVI_3_p8nL_CRfi7YMva7i5hoEiBKPz0uSgULTvdEdT2dbrKomVqeShggp2pszREzXYlx9bzianiEo3-E6ws0_6SucPR6bI3xL6ZpxZSGGVg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html > <https://secure-web.cisco.com/1QMftmSEkoOcMup8n7cdsjGsnt_jh6CcognWlaFpWHLJcs7auJEDBbMJbLRezgiT8UF54ERqSEfWuxhrcKwFcqqNhjMAsmIWiLd2UoPF0seMKkt6Wc0rvdZlYHI6pv0bq7IRXU3xbUXPr4Unz9UigY6jNqDUTsPBnO_8ENIoreFxVI_3_p8nL_CRfi7YMva7i5hoEiBKPz0uSgULTvdEdT2dbrKomVqeShggp2pszREzXYlx9bzianiEo3-E6ws0_6SucPR6bI3xL6ZpxZSGGVg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html>* > will 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, > > $ bash > The 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/1KpUjM8gxP6rhj7QeUI6s-vBJfpLQGND7uvBXrg-UT9JUxIf9tKvwUmOxubVVprJaWJYwyoDY6BmHNFk4lfOp55GSAW9JL1xqYG4ms-aAKEXkO6ZBuQTTrlTNqJceXsRhvJNTRIKcna2-ob4gNGtlDR4Dgq5b83LdiU9hCQT3AGkhVVopatJ1GiJt_RWrSzgaLCmraKNoK7fOCq2UQtUWLr-vwl120YHfqo-gH8COB3ASqpmNRXUJV63gyxCqDzwk0L449ZRE7AXn_qaayU3uSw/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050. > > … reset the SHELL environment to reflect bash ... > > userid@developer-Mac:~> export SHELL=/bin/bash > userid@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/1wNvQu11ahw_8tkmY4IIcTcqOhOfYIu7RG6AW14ug8KW__qIGw3AUpFpYQzaRmBoI2MZeOmXYdEsl4kBThJHu-aDKuSccwgTwS5UVSFElDWNmHFmM-WpIe-0kjPtDqbJuuPaOrAlO2n5SpQH35bVjylaFYq_T9WIMf5rqjln7Z7IQFT_fMColgagEPPhzjjuY25J_8K-HYIJyanj4ejLTOodUZAZXb1VQdZOzbxP3vJSk3lE3go1e-FSF5zFpXLEyryPmzvrhrOmQFnwLac2XOQ/https%3A%2F%2Fsupport.apple.com%2Fen-us%2FHT208050 > <https://secure-web.cisco.com/1wNvQu11ahw_8tkmY4IIcTcqOhOfYIu7RG6AW14ug8KW__qIGw3AUpFpYQzaRmBoI2MZeOmXYdEsl4kBThJHu-aDKuSccwgTwS5UVSFElDWNmHFmM-WpIe-0kjPtDqbJuuPaOrAlO2n5SpQH35bVjylaFYq_T9WIMf5rqjln7Z7IQFT_fMColgagEPPhzjjuY25J_8K-HYIJyanj4ejLTOodUZAZXb1VQdZOzbxP3vJSk3lE3go1e-FSF5zFpXLEyryPmzvrhrOmQFnwLac2XOQ/https%3A%2F%2Fsupport.apple.com%2Fen-us%2FHT208050>* > (e.g.., 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. > _______________________________________________ > Freesurfer mailing list > freesur...@nmr..mgh.harvard.edu > https://secure-web.cisco.com/12vSTKvjUTadMQFZo-5bFzQ2N2j2vHTgF6J_0R7G_BLmyM-bj0bgdHSHPqaOww8V981y4VtxZga0_TqbELe4wcGTVjvekPlMx6oHyLAZe3aLnDxAj3i1NL4ca4lAwmKlRqKelWaxz5lhJ-MdqrvaLbfFZOKnTD89H0QNQKM2VORhb6luyAhlKcLJhyfMWheHItoGt0-WGcA005493p95n698G3AQyFZeMONcQL7fj3Iq2VMJe_C1B7HDC9y83OexbbP2w6R_RgFy7XEb555yAoQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > >
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