External Email - Use Caution
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 <laure...@stanford.edu> wrote:
[CAUTION: Non-UBC Email]
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: laure...@stanford.edu<mailto:laure...@stanford.edu>
P: (650)-725-1716
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