I suspect that recon-all is confused about your SUBJECTS_DIR:

setenv SUBJECTS_DIR /home/tur31606@tu.temple.edu/freesurfer_output

Can you change SUBJECTS_DIR to not include the special characters ‘@’ and ‘.’?

From: andrew cardona <ascardona0908@gmail.com>
Sent: Thursday, June 26, 2025 1:13 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Trouble shooting

        External Email - Use Caution        

Hi, 

thank you for your timely response! this is the output for recon all :s-check-version --s sub-SM --o /tmp/tmp.db9lL9 Thu Jun 26 10:38:52 EDT 2025 setenv SUBJECTS_DIR /home/tur31606@tu.temple.edu/freesurfer_output cd /home/tur31606@tu.temple.edu /home/tur31606@tu.temple.edu/freesurfer/bin/fs-check-version --s sub-SM --o /tmp/tmp.db9lL9 -rwxr-xr-x 1 tur31606 domain users 18565 Jun 13 2023 /home/tur31606@tu.temple.edu/freesurfer/bin/fs-check-version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 $Id$ Linux CLA19571.tu.temple.edu 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux pid 79136 Current FS Version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /home/tur31606@tu.temple.edu/freesurfer/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /home/tur31606@tu.temple.edu/freesurfer_output Actual FREESURFER_HOME /home/tur31606@tu.temple.edu/freesurfer Linux CLA19571.tu.temple.edu 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux /home/tur31606@tu.temple.edu/freesurfer_output/sub-SM mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-SM/sub-10317_T1w.nii.gz /home/tur31606@tu.temple.edu/freesurfer_output/sub-SM/mri/orig/001.mgz mri_convert /data/Project_LITE/Imaging/LITE_PAT/bids/sub-SM/sub-10317_T1w.nii.gz /home/tur31606@tu.temple.edu/freesurfer_output/sub-SM/mri/orig/001.mgz mri_convert: can't determine type of output volume Command exited with non-zero status 1 @#@FSTIME 2025:06:26:10:38:53 mri_convert N 2 e 0.00 S 0.00 U 0.00 P 50% M 6144 F 0 R 270 W 0 c 0 w 2 I 0 O 0 L 0.18 0.27 0.34 @#@FSLOADPOST 2025:06:26:10:38:53 mri_convert N 2 0.18 0.27 0.34 Linux CLA19571.tu.temple.edu 6.8.0-60-generic #63~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Apr 22 19:00:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-SM exited with ERRORS at Thu Jun 26 10:38:53 EDT 2025 For more details, see the log file /home/tur31606@tu.temple.edu/freesurfer_output/sub-SM/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

and for mri_info it just reports back all the stats of the file it has no issue reading it when using mri_info. 

best, 

andrew

On Thu, Jun 26, 2025 at 12:14 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

If you run mri_info on the image, what does it report?

Can you send recon-all.log?

Yujing

From: andrew cardona <ascardona0908@gmail.com>
Sent: Thursday, June 26, 2025 11:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Trouble shooting

        External Email - Use Caution        

Good morning, 

I am trying to troubleshoot one participant, yet It keeps failing and starting this error “ mri_convert : can’t determine type of output volume” we have tried changing the file manually to mgz and it works yet when running recon all it crashes. Any guidance would be appreciated! Thank you in advance! 

Best, 

Andrew cardona 

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