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 ($subj/mri/orig/001.mgz) is intact, suggesting a possible issue during conversion (e.g., mri_convert).
I didn’t find similar reports in the archive, and the problem reproduces identically across both versions of FreeSurfer below. recon-all.log files are attached.
* FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 AND freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 * OS: Rocky 8.10 * uname -a: Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
Any insight would be greatly appreciated. Thank you!
Kindly, Ellie
Ellie Minhae Kim (she/her/hers)
Program Director | Pain and Neuroinflammation Imaging Lab
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 Thirteenth St, Suite 2316
Charlestown, MA 02129
Phone: (617) 643-0569
From the recon-all.log files that you shared, I noticed that you set SUBJECTS_DIR to the same directory for both 5.3.0 and 7.4.1 runs. I think it is better to keep them separate because there are symbolic links under the SUBJECTS_DIR pointing to release specific files.
The FS5.3.0 was built on centos6. Running it on Rocky8 machine might run into some compatibility issues.
From: Kim, Minhae EKIM35@mgh.harvard.edu Sent: Thursday, February 26, 2026 5:17 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Truncated T1.mgz after recon-all
Hello FreeSurfer team,
I encountered an error while running recon-all where T1.mgz files for two subjects appear to be cropped posteriorly along the Y dimension (RAS). The cortex is preserved, but portions of the skull and the scalp are removed. The input file ($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.
* FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 AND freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
* OS: Rocky 8.10
* uname -a: Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
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
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.
* FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 AND freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 * OS: Rocky 8.10 * uname -a: Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
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
freesurfer@nmr.mgh.harvard.edu
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Huang, Yujing -
Kim, Minhae