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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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!