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Dear Yujing,

datadir leads to the folder with one subfolder per participant containing the T1.nii file. There is one folder per subject - and no participant name exists twice.

Angelika

Le jeu. 5 févr. 2026 à 22:43, Huang, Yujing YHUANG43@mgh.harvard.edu a écrit :

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

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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 _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu

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