Hi Yujing,

Thank you for your reply and suggestions.

To note, the outputs were identical for both 5.3.0 and 7.4.1, and recon-all worked fine for all 60+ scans except for two, which, to me, suggests that it’s not an issue with FreeSurfer versions, mapping, or compatibility.

I would welcome any other thoughts or feedback to further troubleshoot this issue. Thank you! 

Kindly,

Ellie


From: Huang, Yujing <YHUANG43@mgh.harvard.edu>
Date: Monday, March 2, 2026 at 11:10 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Truncated T1.mgz after recon-all

From the recon-all.log files that you shared, I noticed that you set SUBJECTS_DIR to the same directory for both 5.3.0 and 7.4.1 runs. I think it is better to keep them separate because there are symbolic links under the SUBJECTS_DIR pointing to release specific files.

 

The FS5.3.0 was built on centos6. Running it on Rocky8 machine might run into some compatibility issues.

 

From: Kim, Minhae <EKIM35@mgh.harvard.edu>
Sent: Thursday, February 26, 2026 5:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Truncated T1.mgz after recon-all

 

Hello FreeSurfer team,

 

I encountered an error while running recon-all where T1.mgz files for two subjects appear to be cropped posteriorly along the Y dimension (RAS). The cortex is preserved, but portions of the skull and the scalp are removed. The input file ($subj/mri/orig/001.mgz) is intact, suggesting a possible issue during conversion (e.g., mri_convert).

 

I didn’t find similar reports in the archive, and the problem reproduces identically across both versions of FreeSurfer below. recon-all.log files are attached. 

 

 

Any insight would be greatly appreciated. Thank you!

 

Kindly,

Ellie

 

Ellie Minhae Kim (she/her/hers)

Program Director | Pain and Neuroinflammation Imaging Lab

 

Athinoula A. Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 Thirteenth St, Suite 2316

Charlestown, MA 02129

Phone: (617) 643-0569

https://loggialab.mgh.harvard.edu/