Dear Zeke, Thank you for pointing in the right direction. As a reminder the problem was that I was not getting the brainmask.mgz file, in the meantime I tried to re run finally got it . \
However, I am surprised of the duration of recon-all -all -openmp 8 (using a linux workstation with 8 cores (2 processors with 4 each). Running 5 subjects simultaneously took up to 52 hours. 4 subjects around 40 hours.
Any way I am attaching the recon-all.log file just to be sure that there are no strange errors. Thank you so much, Pablo
Date: Mon, 16 Dec 2013 17:18:32 -0500 From: zkaufman@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu; pablonajt@hotmail.com Subject: Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz
Pablo,
I need the recon-all.log file located in the $SUBJECTS_DIR/scripts directory. Sorry for the confusion.
-Zeke
On 12/13/2013 04:48 PM, pablo najt wrote:
Dear Zeke, Thank you so much. As I am not sure which is the log file that we use I am attaching mri_nu (in mri directory) and talairach_avi (in mri/transformations directory). Thanks, Pablo
Date: Fri, 13 Dec 2013 16:21:48 -0500 From: zkaufman@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Output of recon-all -all -openmp 8 does not
show brainmask.mgz
Hello Pablo,
Please send me the recon-all.log file for the subject and I will take a look.
-Zeke
On 12/13/2013 03:41 PM, pablo najt wrote:
Dear FS, I am checking on the outputs of recon-all -all using the flag
-openmp 8.
As I did with standard recon-all -all comand line I was trying to check brainmask.mgz, but there is not such file. Is there anything wrong with my outputs? Or I should be checking a different file? Thank you, Pablo
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