External Email - Use Caution
Hello Joann, If I read correctly, you are doing a remote mount of a shared network drive to your Mac to store/read/write the subject files but running the recon-all using your Mac processors. You might want to check the directory for the last subject processed to see if there are log files with any more info. A segmentation fault can happen for various reasons, but we might be able to tell something if you can get a hold of the core dump file. There could be differences w.r.t how Ventura maintains a connection to and interacts with a remote file system compared to Monterey, e.g., timeouts, authentication, file caching, etc . If recon-all was proceeding normally and then no longer could see or access the remote file system when it needed to read or write a file, then the recon-all would fail. But I would expect to see some message w.r.t file not found, permission denied and not just a segfault message.
We have have not done any testing with MacOS Ventura and we don’t generally test on MacOS using remotely mounted file systems. Many Mac users I know always stay one operating system release behind the latest version of MacOS. They are only now upgrading from BigSur to Monterey since Ventura was officially released last month. If I have test the latest release I try to wait until the first .1 release is out as the initial .0 releases are often the most buggy (for Ventura that would mean waiting for 13.1). - R.
On Nov 7, 2022, at 17:27, Joann Stewart <stewart.joann3@yahoo.com> wrote: External Email - Use Caution Hello, I am attempting to analyze some structural morphometry data. I am having issues with the recon-all command that I am using. I am attempting to run this command on a shared network folder through my institution. Here is the exact command I am using : recon-all -subject 1306_A -i 1306/T1w/T1w_MPR.nii.gz -T2 1306/T2w/T2w_SPC.nii.gz -T2pial -all -qcache On the server, when I run this command, it continues until I get to the segmentation portion. I have the full output of this command attached to the email in a word document titled “Recon-all output on server”. Attached I also have a copy of the recon-all.log file. There is another member in my lab who was able to use this command successfully with the same files and exact same code. He was using the same server that I was on, and we have exactly the same permissions on the server. The only difference is that I have updated my mac to Ventura and he has not yet updated his mac (he is using macOS Monterey 12.6). We tried moving my files onto my desktop to see if the recon-all worked there as compared to the server. I simply moved the T1w & T2w NIfTI files onto my desktop from the server. When I run recon all sourcing from the NIfTI files on my desktop rather than the server, it works fine without error. Therefore, we are wondering if it is an issue with the new Ventura update in conjunction with shared network folders. Do you have any suggestions or ideas based on the information I have provided? FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275Platform: MacOS Ventura 13.0 Let me know if there is any more information that you need. Thank you!<Recon-all output on server.docx><recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B