'-careg' probably is not needed for autorecon3 if it is run separately after autorecon2.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Tuesday, March 7, 2023 10:53 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR: cannot find or read transforms/talairach.m3z

Hi,

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

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fraser Aitken Sent: Tuesday, March 7, 2023 10:45 AM To: freesurfer@nmr.mgh.harvard.edumailto: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