When you run recon-all, it will create a recon-all-status file in the scripts directory. This has the start times of all the processes, so you can work out how long each took. This will be wall clock time, so take that into account.
doug Leo Souza wrote: > Hi Carolina, > > Do you know how can I run Freesurfer just to get some Benchmark > Numbers and to Check GPU Performance using Cuda? > > Thanks, > *Leo Souza* > > On 06/13/2011 07:04 AM, Carolina Valencia wrote: >> Thanks a lot, it works. >> just waiting 24 hours. >> >> Best regards, >> >> Carolina >> >> 2011/6/10 <rspr...@nmr.mgh.harvard.edu >> <mailto:rspr...@nmr.mgh.harvard.edu>> >> >> Hi Carolina, >> >> Sorry My bad. I was inaccurate in my previous message. >> >> -subject should work. >> >> Assuming that the MPRAGE of your subject is under the following >> directory: >> >> /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig >> >> set your SUBJECTS_DIR to >> /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig >> before >> running recon-all >> >> setenv SUBJECTS_DIR >> ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig >> >> recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject >> $SUBJECTS_DIR/hptu_subj001 >> >> This should create a folder where Freesurfer recons will be created: >> >> cd >> >> ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001 >> >> Best, >> Priti >> >> > Hi Carolina, >> > >> > -subject is not recognized by Freesurfer...Use -subjid or -s >> instead. >> > >> > setenv SUBJECTS_DIR <path to tutorial data> >> > >> > recon-all -all -i <path to your MPRAGE>/MPRAGE.nii.gz -s <path to >> > freesurfer recons>/hptu_subj001 >> > >> > Priti >> > >> >> Hello Freesurfer's users, >> >> >> >> I'm starting using FS and I have a problem running recon-all >> >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz >> >> within >> >> tutorial_subj >> >> First I convert nii.gz to mgz qith the command: >> >> recon-all -i MPRAGE.nii.gz -s hptu_subj001 >> >> and then in order to process all, I type: >> >> recon-all –i 001.mgz –subject hptu_subj001 –all >> >> >> >> >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> >> >> recon-all –i 001.mgz –subject hptu_subj001 –all >> >> ERROR: Flag i unrecognized. >> >> i 001.mgz subject hptu_subj001 all >> >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> >> #50-Ubuntu >> >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 >> >> >> >> then I tried with: >> >> >> >> >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> >> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all >> >> ERROR: Flag i unrecognized. >> >> i MPRAGE.nii.gz subject hptu_subj001 all >> >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> >> #50-Ubuntu >> >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 >> >> >> >> How I can fix this error? >> >> >> >> Thanks a lot, >> >> >> >> Best regards, >> >> >> >> Carolina >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto: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. >> >> >> >> >> -- > This email message is for the sole use of the intended recipient(s) > and may contain confidential information. Any unauthorized review, > use, disclosure or distribution is prohibited. If you are not the > intended recipient, please contact the sender by reply email and > destroy all copies of the original message. > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
