I don’t know what your ${datadir} looks like. You submitted recon-all for each entry in the ${datadir}. Make sure the ${subj_id} derived from the subdirectory is unique for each recon-all submission.

Yujing

From: Angelika Wolman <angelikawolman67@gmail.com>
Sent: Thursday, February 5, 2026 4:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Re: recon-all doesn't find 001.mgz in mri/orig

        External Email - Use Caution        

Hello FreeSurfer Developers,
 
I'm attempting to compute recon-all on my nii files.
It seems it doesn't find 001.mgz in mri/orig



Subject does not have a bstampfile, copying /opt/fox_cloud/share/app/imaging/freesurfer/7.3.2-1/build-stamp.txt
 
 
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 
 
1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275  Platform: Linux  PlatformVersion: 3.10.0-1160.119.1.el7.x86_64  CompilerName: GCC  CompilerVersion: 4.8.5


2) Platform: CentOS Linux release 7.9.2009 (Core)
3) uname -a: Linux fox-c18 3.10.0-1160.119.1.el7.x86_64 #1 SMP Tue Jun 4 14:43:51 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
 
4) recon-all.log: see attached
5) script used: attached (T1_recon_all2.sh)

Thank you !

Angelika