External Email - Use Caution Below are the commands I used to run freeview from the Freesurfer 7.4..0 release on a silicon Mac with an M2 processor running MacOS Sonoma 14.7.2 with Xquartz 2.8.5. I put the freesurfer license.txt file under my home directory and set the FS_LICENSE environment variable to its path. (If you add that FS_LICENSE setting to your shell initialization file, then you should not need to worry about setting up the license again no matter what freesurfer release/build you end up using). I then ran freeview with no arguments to make sure it could open an empty window. Then I had freeview display one of the volume files included with the example subject data. The old 7.4.0 release contains only Intel binaries and so has to run under Rosetta on silicon Macs with M processors. While this should work for freeview, it will not work to run some of the other commands in the 7.4.0 distribution on a silicon Mac. If you plan to use the freesurfer mri* commands, then you would be better off installing a native build of freesurfer compiled for the silicon Macs. You can use this installer package to install a recent stable development build from 09/2024, https://secure-web.cisco.com/1mYajo-Nb3fUswwrx78iSXy97lDpj0Dp8I08BqN2A2fqgcq_b7Xg5hGDXaNDqfQxBslJeO6nnmL5j-qDdfuyaAZB4y4cG9yxmNymVOiPmt-CRJ9dIupSNylRgxbNqxgekoG3sHmC8IZflWYfK5beVMf7-7QGkYckb1Gvcl930x4l3iycxnVRU645tzLGA8Cm0vkX6kpjjCZuvnVXlsfSgdPIs4iGkkE8R3gM4SzglpYyKiXEVHW3Q6Z36eiZTugVHaBmx0z2K7A8uYO9APT30BvcW31Kboxq_8okHkLPEj9-FiuTaFkmJWsouNv_VjwmVn363k-AFZ1DpScflE9X4GQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2Ffreesurfer-macOS-darwin_arm64-dev.pkg If you want to try that development build, I would first remove the 7.4.0 release with the command,$ sudo bash /Applications/freesurfer/7.4.0/uninstall.sh With that development build, then FREESURFER_HOME would be set as in the commands below as,$ export FREESURFER_HOME=/Applications/freesurfer/dev - R. - - - - - - - $ bash… output deleted …$ export FREESURFER_HOME=/Applications/freesurfer/7.4.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.4.0-20230510-e558e6e --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Applications/freesurfer/7.4.0FSFAST_HOME /Applications/freesurfer/7.4.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Applications/freesurfer/7.4.0/subjectsMNI_DIR /Applications/freesurfer/7.4.0/mni$ which freeview/Applications/freesurfer/7.4.0/bin/freeview$ export FS_LICENSE=$HOME/license.txt$ head -1 $fs_license...@somewhere.com <—— email address you used to register for license$ freeview <—— check that freeview opens an empty window$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz <--- try opening one of the included volume files On Jan 3, 2025, at 00:49, Tietze, Anna <anna.tie...@charite.de> wrote: External Email - Use Caution M3 max processor Anna
Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von fsbuild <fsbu...@contbay.com> Gesendet: Donnerstag, 2. Januar 2025 19:46 An: freesurfer@nmr.mgh.harvard.edu Betreff: [ext] Re: [Freesurfer] Freeview crash External Email - Use Caution Are you running on an old Intel Mac or a Mac with one of the newer M1, M2, M3, M4 processors ? - R. On Jan 2, 2025, at 13:02, Wang, Ruopeng <rwa...@mgh.harvard.edu> wrote:Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this: $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tie...@charite.de> wrote: Hi, When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me? Operating system: Mac, Sonoma 14.7.1Fressurfer version 7.4.0XQuatz 2.8.5licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works)environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh When I run the command freeview, the following message is given:/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Or trying to open a file:freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview..app/Contents/MacOS/freeview "$@" Attached is a detailed error report. What did I overlook?? Thank you so much for help! Best, Anna<problem report freeview.rtf> External Email - Use Caution _______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1QHuUffDuUmCT6Kur8brjyEtinGdgVAQ8kT19o05mNUMnZk4SRTfrbbiRGpm_c7ZvvdpcW3zCzQmVAc6ZukNIUnZkgtBzEu05rZqBYbAUGTScFQSGxSjpTJEasXOVXZa2IpWO0s9qKm-sSlw5mR-BnaIZ6g5xPUeMtDJfAmWgKZfgtjh1o245Z0hBLstsUJuMJuRPFXO8gHpP_JYe304UZWNjcSIuSb7IDeTRDxL3H_nzt9ZnWsAJj8JmfLTXvLcVbe4ypCBkAs_bilpULshjWZBvowxJ1uF-G6RRgfcHpDzL-pgslbubhrhxPckF_d7PJeAfPUHYVGPda3IVv8D0bQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1QHuUffDuUmCT6Kur8brjyEtinGdgVAQ8kT19o05mNUMnZk4SRTfrbbiRGpm_c7ZvvdpcW3zCzQmVAc6ZukNIUnZkgtBzEu05rZqBYbAUGTScFQSGxSjpTJEasXOVXZa2IpWO0s9qKm-sSlw5mR-BnaIZ6g5xPUeMtDJfAmWgKZfgtjh1o245Z0hBLstsUJuMJuRPFXO8gHpP_JYe304UZWNjcSIuSb7IDeTRDxL3H_nzt9ZnWsAJj8JmfLTXvLcVbe4ypCBkAs_bilpULshjWZBvowxJ1uF-G6RRgfcHpDzL-pgslbubhrhxPckF_d7PJeAfPUHYVGPda3IVv8D0bQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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