Hi,

Can you try adding '-careg' to your recon-all command line after -autorecon2/-autorecon3?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fraser Aitken
Sent: Tuesday, March 7, 2023 10:45 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: cannot find or read transforms/talairach.m3z

        External Email - Use Caution        

Hi all

I have upgraded to 7.3.2 and i seem to be having issues running recon all after unto recon1. Basically, auto recon completes but after I have checked the brain masks and go to run auto recon 2 and 3 i get the following error

reading 1 input volumes

reading classifier array from /usr/local/freesurfer/average/RB_all_2020-01-02.gca

reading input volume from norm.mgz

average std[0] = 7.2

reading transform from transforms/talairach.m3z

ERROR: cannot find or read transforms/talairach.m3z

error: No such file or directory

error: transforms/talairach.m3z: could not open transformCommand exited with non-zero status 255

@#@FSTIME  2023:03:07:14:29:54 mri_ca_label N 10 e 15.23 S 0.25 U 14.96 P 99% M 498868 F 9 R 123462 W 0 c 42 w 348 I 1568 O 0 L 1.48 1.71 1.24

@#@FSLOADPOST 2023:03:07:14:30:10 mri_ca_label N 10 1.37 1.67 1.24

Linux bioeng342-pc 5.4.0-144-generic #161-Ubuntu SMP Fri Feb 3 14:49:04 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s Freesurfer exited with ERRORS at Tue Mar  7 14:30:10 GMT 2023

This is the command I am using to run the skull strip

reconAllCommand = sprintf('recon-all -i %s -subjid ''Freesurfer'' -autorecon1 -multistrip -cw256 -cm',T1File);

and these are the other commands

 % run autorecon2

        reconAllCommand = 'recon-all -subjid ''Freesurfer'' -autorecon2 -cm';

        unixCommand = sprintf('%s\n%s',subjectDirCommand,reconAllCommand);

        unix(unixCommand);

        % run autorecon3

        reconAllCommand = 'recon-all -subjid ''Freesurfer'' -autorecon3 -cm';

        unixCommand = sprintf('%s\n%s',subjectDirCommand,reconAllCommand);

        unix(unixCommand);

        % copy Freesurfer output to rootDir

        sourceDir = fullfile(Freesurfer,'Freesurfer');

        targetDir = fullfile(rootDir,'Subject_data',subjects{iSubj});

        unixCommand = sprintf('cp -r %s %s',sourceDir,targetDir);

        unix(unixCommand);

Greatful for any suggestions of a fix