What was your recon-all command line? You need to give it a directive (like
-all), otherwise it will just create a subject directory tree and put the
001.mgz in the orig dir
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Naama Zur
Sent: Sunday, March 17, 2024 5:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all command produces only 001.mgz file in the
mri/orig directory
External Email - Use Caution
Hi all,
I am using Ubuntu 23.1 with freesurfer 7.4.1 to run the recon-all command and
the command runs without error and I do get a set of directories including:
label, mri, scripts, stats, surf, tmp, touch, and trash. However, the only
folders that are not empty are scripts where there are 11 files and a 001.mgz
file in the mri/orig directory.
I am not sure what I am doing incorrectly and was hoping for some guidance with
this.
Thank you!
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