Re: [Freesurfer] Recon-all completed without error in 10 seconds

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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 E: laurenss@stanford.edumailto:laurenss@stanford.edu P: (650)-725-1716

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