The Freesurfer ‘recon-all’ script writes that message to ‘stdout’, not 
‘stderr’, thus it shows up in the *.o* file from your cluster management 
software, not the *.e* file.  i.e., you need to look at both to debug problems.


Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email:

From: YC Yao <<>>
Date: Friday, October 14, 2016 at 10:57 AM
To: Michael Harms <<>>
Cc: "<>" 
Subject: Re: [HCP-Users] errors with HCP_Pipelines structural processing

Thank you for your prompt replay!

I noticed that “error” message before, but it resides  in which is the output logging file but not in which is the error message file. Therefore, I 
assume that it will not do harm to the result.

I believe I have deleted all files except the unprocessed directory where the 
example data resided. I will try again later.

Thanks again!

Best regards,
YC Yao

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