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I think you need to pass the flag ‘-all’ in the command line.

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

Nárlon Cássio

Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSHR BC/CLEAR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon

On Sep 13, 2023, at 2:01 PM, Lauren Stephens <laurenss@stanford.edu> wrote:

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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  
P: (650)-725-1716

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