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: pablon...@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: zkauf...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu; pablon...@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: zkauf...@nmr.mgh.harvard.edu > > > To: pablon...@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 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.
