External Email - Use Caution        

Hi Yujing, 

Thank you, that did work! 

Follow up question: Why would the code I used above, successfully generate the recon-all outputs for our other files?

Thanks, 

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


From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Wednesday, September 13, 2023 11:05 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds
 

        External Email - Use Caution        

Hi Lauren,

 

You will also need to specify ‘-all’ to recon-all.

 

Best,

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lauren Stephens
Sent: Wednesday, September 13, 2023 2:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all completed without error in 10 seconds

 

        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