Hi Kilian, I'm wondering what were your initial recon-all commands for FS 5.3 and FS 7.1.1 because I'm not sure '-autorecon1' is making mri_ca_register call by default.
But It looks like you can use '-careg' to turn on mri_ca_register call. Here is a description of recon-all steps: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all Best, Yujing -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Kilian M Pohl Sent: Wednesday, December 7, 2022 12:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] ma_ca_register is not called anymore in version 7.3.2 External Email - Use Caution Hi , I have used the following call starting at Freesurfer 5.3 /usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon1 -noskullstrip -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234 It is still working with Freesurfer 7.1.1 but we now tried updating to 7.3 and it is failing (on the same case). Looking at the recon-all.log it seem that ma_ca_register is not called anymore so that I get the following error message ERROR: cannot find or read transforms/talairach.m3z (see attached recon-all .log) Do I have to add flags ? I need to run with -noskullstrip Best, Kilian -- Kilian M. Pohl, Ph.D. Associate Professor Department of Psychiatry & Behavioral Sciences Stanford University 401 Quarry Road Stanford, CA 94305-5717 https://secure-web.cisco.com/18F69KCiyMWMSCouFYLrT3r9PgA1L7oUNzDa59-gQWUTsShFpsrS5hQaNO0pEiGsaHKqzn0e7h779L6bRMyMzCb5lAaJ0fwqBPOW8lLemFVir4TX77sLrDhxEwmH-_K67k8Wcj5yqqwssCRe30iCQlZMOzk85FBTQjdmczVPEVeGst3kfkscpPmkXiXo-cwSGKJXv1R11Ewgyiwc5CjQCPFAqtUjQeb7euLkZkt3-C8o6obbJ0vMPi_LRo-acT8JTG3md3jIZp5SKjkGKtcMoXGHrFwNJDMhft67lw3HEeOS622OvlwvJ-uB9Pag7DGyNwYPOk96CddmcVnHow7dIvw/https%3A%2F%2Fweb.stanford.edu%2F%7Ekpohl _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
