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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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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
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