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Hi,

I’m using macOS big sur 11.5.2. The file did exist and I do have read permissions; I also did resolve the problem eventually :) - I had a backup of fs and replaced the whole subject directory with it and now recon-all seems to be working fine. Thank you for your help.

I have another problem I cannot seem to solve and would appreciate your help with though - can I run matlab runner through fs on mac? The installation goes on without problems (fs is 7.2.0. and matlab is v84) and matlab starts to process my recon-all’d files, however it never finishes with success. I’ve read that big sur does not work with versions of matlab as old as the one that fs installs, however I don’t know how to install the newer ones through fs. I need to know volumes of hippocampal segments for my research project and cannot work my way around the problem with matlab here.

Thank you very much for your help,
Agata Szulia

On 6 Sep 2021, at 20:13, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

What platform are you using (eg, mac?). Can you send the recon-all.log file? Can you verify that the file actually exists and that you have read permissions?

On 9/3/2021 4:52 AM, Szulia Agata wrote:
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Hi,

I have a problem with running recon-all on some subjects. Mostly, it does exit without errors, however sometimes it exits with "ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version”. I have only one version of fs installed - 7.2.0. Does anyone know why does it happen and how to proceed with recon-all in such cases?

I attach recon-all log files.

Thank you very much for your help,
Agata

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Klauzula poufności. Ta wiadomość pocztowa i wszelkie załączone do niej pliki są poufne i podlegają ochronie prawnej. Jeśli nie jesteś jej prawidłowym adresatem, jakiekolwiek wykorzystanie w tym zapoznanie się z treścią przesłanych informacji, jej ujawnienie, reprodukcja, dystrybucja lub inne rozpowszechnienie, są ściśle zabronione. Jeśli otrzymał/a Pan/i niniejszy przekaz wskutek błędu, proszę o niezwłocznie powiadomienie nadawcy i usunięcie otrzymanych informacji. Kontakt: Uniwersytet Medyczny w Łodzi, 90–419 Łódź, Al. Kościuszki 4, Rektorat – Centrala, Tel. 42 272 59 66 umed.lodz.pl Confidentiality Notice - This e-mail is confidential, may be legally privileged. If you are not the intended recipient, you may not use, disclosure, distribute, copy, print or rely on this e-mail. If you received this e-mail in error, please notify the sender and delete the material from any computer.Contact:Medical University of Lodz, 90–419 Lodz, POLAND, 4 Kosciuszki Avenue, Rector’s Office, phone 0048 42 272 59 66 umed.lodz.pl