Hello Lauren:

Open the sR0391178-0002-00001-000208-01.nii.gz file using freeview and see if the whole 3D brain is in place. This should give you a clue as to why this occurred.

best,

Alan

On Wed, Sep 13, 2023 at 1:02 PM Lauren Stephens <laurenss@stanford.edu> wrote:

        External Email - Use Caution

Hi Freesurfers,

I am attempting to run recon-all on a set of .nii.gz files. Each file is in our subject directory and has run through recon-all. Recon-all only takes 10 seconds to run and says it was completed without errors. When I go to the folder recon-all creates, the folders are empty.

Here is the code we ran:

recon-all -s 967 -i /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz

Here is the output message:

Started at Wed Sep 13 10:52:44 PDT 2023

Ended at Wed Sep 13 10:52:54 PDT 2023

#@#%# recon-all-run-time-hours 0.003

recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023

done

We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 7.3.2.

I have attached the recon-all.log file and would appreciate any suggestions. We have previously run many successful recon-all's and have not encountered any issues.

Thank you,

Lauren Stephens

Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laurenss@stanford.edu

P: (650)-725-1716

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Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience

University of Texas, School of Medicine

Rio Grande Valley

Texas.