Hi Zixuan,

I would try keeping the input and output folders separate (i.e., use a different output folder). Also, usually we don’t need to specific the subject’s directory in the command line if it’s already set up in the environment.

Nárlon Cássio

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zixuan Lin <zlin14@outlook.com>
Reply-To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, July 13, 2022 at 8:53 PM
To: "freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all finished without error but no results

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Hello!

I am trying to run recon-all but it only converted the original image to .mgz and finished without error. I checked all other folders and it's empty. Attached please find the recon-all.log.

The command line I used is

recon-all -i hc01.nii -s hc01 -sd /home/zlin/Documents/MDD_CVR/control

Could you please help me check what happens here?

Thanks a lot,

Zixuan.