External Email - Use Caution
Thank you very much, that seemed to work out well.
Freeview is working and I run the recon all on bert (which was not there?) until it suddenly exited.
Segmentation fault
ERROR: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta bert
Darwin Markus-Gschwinds-MacBook-Pro-2.local 23.6.0 Darwin Kernel Version 23.6.0: Mon Jul 29 21:14:46 PDT 2024; root:xnu-10063.141.2~1/RELEASE_ARM64_T6031 arm64
recon-all -s bert exited with ERRORS at Thu Aug 21 22:01:25 CEST 2025
Any ideas?
Thank you in advance! Markus
On Thu, Aug 21, 2025 at 2:53 AM fsbuild fsbuild@contbay.com wrote:
External Email - Use CautionHello Markus,
I don’t expect 5.3.0 to work correctly on a new silicon Mac so I would delete 5.3.0 from the new machine. If you need to continue to do work with and/or verify results with 5.3.0, then continue to run it on your old Intel Mac.
Unfortunately, the video you watched is somewhat out of date; it may not work on a silicon Mac with a newer version of MacOS to launch freeview via the Finder so you should try the command line instead (see below).
The most recent info on Freesurfer updates is on,
https://secure-web.cisco.com/1OxsA8p_vWFvg1FYCljBmQCFtgsyUvVjq4JJxnpk3cSVILP...
In the section describing the 8.1.0 release, the “here” link for setup information points to,
https://secure-web.cisco.com/1xiEOuQEAQrnCLoU6aOljuyoCy8cTxPl0qzlldZLKdWvwNo...
You should setup your license file to be found in the shell environment via the FS_LICENSE environment variable as described in the 1st section SEETUP FREESURFER LICENSE
The section further down the page in SETUP A MATLAB DISTRIBUTION for MACOS lists how you should set the freesurfer environment. Please try running the bash shell as listed, and I’ve essentially listed all that below. Once the bash shell output resembles the below, try running freeview from the command line.
- R.
…. create a new terminal window and run the bash shell … in the output below the users home directory ($HOME) is /Users/me ...
me@MyMac ~ % bash
The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://secure-web.cisco.com/18zKlfkzooun8OMtEeVds_4RmaNUpR3OojRUNFgQ2NNWbAQ...
me@MyMac:~$ export FREESURFER_HOME=/Applications/freesurfer/8.1.0
me@MyMac:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_arm64-8.1.0-20250718-f30dfed -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/8.1.0 FSFAST_HOME /Applications/freesurfer/8.1.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/8.1.0/subjects MNI_DIR /Applications/freesurfer/8.1.0/mni
…. if you setup FS_LICENSE as listed via the instructions in the setup section of the URL listed above, you should see …
me@MyMac:~$ echo $FS_LICENSE /Users/me/license.txt
me@MyMac:~$ ls $FS_LICENSE /Users/me/license.txt
… test running freeview ...
me@MyMac:~$ which freeview /Applications/freesurfer/8.1.0/bin/freeview
… make sure an empty window opens …
me@MyMac:~$ freeview
… if that worked, then try loading a volume …
me@MyMac:~$ freeview $FREESURFER_HOME/subjects/cvs_avg35/mri/brain.mgz
You can ignore any notifications about methods/classes w.r.t window functions.
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