Pablo,
I do not see the attachment. It may have been filtered because the freesurfer list has fairly strict file attachment size restrictions. Feel free to send me the recon-all.log directly at zkaufman@nmr.mgh.harvard.edu
However, depending on the processor, I am not surprised your ~10hr runtime per subject timeline. Based on documentation that I have seen, you can really only expect about 25% decrease in the time it takes to run recon-all when using the "openmp -8" flag. This because only some parts of the freesurfer code are parallelized. Which means that if you were not using the openmp flag, you should be having about 13.33hrs/subject, which is a valid ballpark estimate of the time it takes to run the recon-all stream on todays machines.
-Zeke
On 01/09/2014 11:44 AM, pablo najt wrote:
Dear Zeke, I am forwarding the email below that I believe it got lost in the dense list of correspondences. I would highly appreciate your input. Thanks, Pablo
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer