External Email - Use Caution
The path /Applications/Freesurfer/dev/bin in the log indicates a development build is running. Since that could be unstable, you could try installing and running the 8.0.0 release, https://secure-web.cisco.com/1q_jK67tubl-gK663E2lJ1Cv-nNx2UB7fhRxZMVS2UCp5EN... But with either the 8.0.0 release from 2/2025 or subsequent dev builds, the machine may not have the resources to run the new recon-all setup. MacOS may kill any process that is too greedy for system resources - which is consistent with the message in the log. The 8.0.0 release and subsequent dev builds requires at least 16G of RAM for recon-all on top of what MacOS plus any other programs are currently using for memory. That could translate to a minimum of 24G of RAM ; the 8.0.0 release was tested on Macs with not less than 32G RAM with no other applications running. So you could also try reverting to the old recon-all behavior from the 7.X releases by setting the environment variable FS_V8_XOPTS on the recon-all command line, e.g., $ export FS_V8_XOPTS=0 && recon-all -all -i I50 -s Subj001 - R. On Jun 2, 2025, at 04:53, nil ahmadi <naiaddiamond1998@gmail.com> wrote: External Email - Use Caution Hello FreeSurfer Developers,
I am running FreeSurfer on my MacBook Air with macOS Sequoia Version 15.5 (ARM64 architecture). I am processing subject 100206 using the recon-all pipeline with T1w and T2w images from my data directory located on an external drive.
However, during the process, the step involving mri_synthstrip fails with the following error message:
mri_synthstrip --threads 1 -i /Volumes/MyDRIVE/freesurfer_output/100206/mri/orig.mgz -o /Volumes/MyDRIVE/freesurfer_output/100206/mri/synthstrip.mgz Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /Volumes/MyDRIVE/freesurfer_output/100206/mri/orig.mgz Processing frame (of 1): 1 Killed After this, the recon-all command exits with errors at Thu May 29 09:27:14 CST 2025.
Here are some details about my setup:
FreeSurfer version: dev version built May 26 2025 (freesurfer-macOS-darwin_arm64-dev-20250526-d84643b) Platform: macOS Sequoia Version 15.5 running on Apple Silicon (ARM64) Hardware: MacBook Air (Apple M3) Data location: External drive mounted at /Volumes/MyDRIVE with sufficient free space (4.4 TiB available) Memory status: System has some paging/swapping activity (vm_stat output attached)
I have attached the recon-all.log file from
Could you please advise on how to resolve this SynthStrip “Killed” error?
Any suggestions on running FreeSurfer successfully on macOS 15.5 with Apple Silicon would be greatly appreciated.
Thank you very much for your support.
Best regards,
Niloufar Ahmadi