External Email - Use Caution
Please send along the link to the video you were using so we can check the instructions. The license is just a single file you obtain by filling out the web form, https://secure-web.cisco.com/1hH-N_TseC854TUMeRYHcee_7ls4Btyl5Nn0kU16Lq7t0_WRhRklCJAoLikm5uceIyi1hFacTs4IWobBeVIm4-6bpWg5I8b6mI5Lh4aD55bFlM6e2kRQqBG52zhINJnsJ3vLYIItoe-DIcD54-e_BsVP5ks7-QDYOsss343875Dlse9QsqNHQJdYOvBIZ7BVRpmfq7WQXHeCBByIdAG6cPGw3ssjgclE_LpsTMmW6EQ84lkZ2RWEA1N37mwSsENt4nhoczNWHtCmcnGMAXJKgBBnxCOpiJj9ox8Nb_vyesBvW_BI7QD_CkZV0Y98qL_2amjPSDQx6ztKUT8eMlun4Ig/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html If the form submission is accepted, the screen will be refreshed and you will see a new page saying your license has been sent to the email address you specified. Assuming you are on a Mac reading your email, the default location for downloads is your Downloads folder. When you receive that email, you can save the license.txt file attached to the email to the default location. It will be saved to $HOME/Downloads which you can see in the Finder Window when you open your Downloads folder - or from the terminal. Open a new terminal window and check/setup the license.txt file, $ cd$ pwd/Users/<your userid> $ ls -l Downloads/license.txt-rw-r—r--@ 1 userid group 71 Aug 10 12:53 Downloads/license..txt <— your userid, group, date, etc. will differ Copy that to your home directory with this command (that is a space followed by a period at the end of the line). Or you could move it in the Finder. $ cp -p -f Downloads/license.txt .$ ls -l license.txt-rw-r—r--@ 1 userid group 71 Aug 10 12:53 license..txt <—— your date, etc. output will differ The above only needs to be done once. To tell freesurfer where to find the license file, you can use the environment variable FS_LICENSE. You set that in your terminal session with the following (using the default zsh = bash compatible shell). $ export FS_LICENSE=$HOME/license.txt I’ll assume you used one to the .pkg installers we provide for the Mac releases, which you can download from https://secure-web.cisco.com/1W8vsqGghiuM0oaEbdbdwmxzEGH9qLKdqIXhIsl6GKqRgPDAiv3DM5VbrFqFNW9iZia1ozEciC_PmdyfKLETlphofFIMWl6FUnwvhfyITT6goytCKFLhXZ0cPZxgaCIczfQ6i-8uL6AHiTXDsby0p_44rtHnlbLlnALH0cEW_6KCOzTTmVIh063iej0vam3EvRdGd0u5-8kqUg9HjRixn0qW3n4Jm8w_W0Ca2C_4acipdySKzGtrhF_qd5tyhHRpkoApa1eA2yP8GIcGz7pYlcbPbXylyniPeiGTapgt6xT9tZYFk52gvmoRfGRaeVsPR6WU6emaWdgzd10kxOZ25nQ/https%3A%2F%2Fsurfer.nmr..mgh.harvard.edu%2Ffswiki%2Frel7downloads If you downloaded the latest 7..4.1 installer, https://secure-web.cisco.com/1hOOmlU9howzc7Jw9g6LR2G-cR50zejLhJkRg9HTIpsOaCQLhnYDrWyhgpy3sogHQQVDvZzOXQmW4aO0aZ6Gd_0UMAn9OdDcnBQPZ0PbxomWPbduAWRLVigW68SpbyT_bv85QW9TX7MgLaPEQOalmSP4vq8rU3jWELRSqL1XHAbdr2wMGqnT_Y-l_vu7mx56fzRIjCGowuihctOquP8ZQSqHD86E4QMEPasn44wjSBeMhl9sluP21Ifj4k7BC-XmooeFA9pq6SurIoLJsW26dyI2ABrtLm33kNkKsUOAX8X32yUMiXUlXX1iY2B99MqqzdPUGA4Wl1vxc5LCfy5llxA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg, - then freesurfer was installed under /Applications/freesurfer/7.4.1 You can navigate to /Applications/freesurfer in the Finder and see what your directory is there under Applications/freesurfer. You will need to add what you find under /Applications/freesurfer to substitute for 7.4.1 in the example below if you did not install the 7.4.1 .pkg. Check our setup script is there in the installation$ ls -l /Applications/freesurfer/7.4.1/SetUpFreeSurfer.sh-rwxr-xr-x 1 root wheel 1350 Jun 14 00:09 /Applications/freesurfer/7.4.1/SetUpFreeSurfer.sh Once you have verified the above path to the freesurfer installation, then setup the freesurfer environment with, $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1 <— change 7.4.1 etc. to be what you installed if different$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Applications/freesurfer/7.4.1FSFAST_HOME /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Applications/freesurfer/7.4.1/subjectsMNI_DIR /Applications/freesurfer/7.4.1/mni Try running freeview with no arguments and verify that it opens an empty window. It should not crash given FS_LICENSE is set above. … check freeview is there ..$ which freeview/Applications/freesurfer/7.4.1/bin/freeview $ freeview… should open an empty window … then manually quit freeview … Try opening one of the example subject volume files $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz … and you should see freeview display some images. - R. On Aug 10, 2023, at 12:03, Aqeel Mohamed <aqeel.t...@gmail.com> wrote: External Email - Use Caution Hello,I am a new Freesurfer user and am currently struggling to run the freeview software on my MacBook Pro Ventura 13.5 OSX.I was following the step-by-step guide video on the Freesurfer wiki, but when it came to opening the 'bert' file, freeview would immediately crash (details of the report below). I unfortunately am a bit inexperienced with computers so I am unsure what the report means so would greatly appreciate any insight you can provide! I am also struggling to create a .license folder via terminal for my license key. I had hunted through the archives of the mailing list and managed to find a pico command but it is not letting me save the folder so would appreciate some help with this too!Apologies for such trivial questions - greatly appreciate any help you can provide!Aqeel
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