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