From: pablonajt@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Thu, 19 Dec 2013 15:27:11 +0000
Subject: Re: [Freesurfer] Output of recon-all -all -openmp 8 does not show brainmask.mgz
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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