Try adding -use-cuda to recon-all Leo Souza wrote: > Yes, I did that, but it doesn't actually uses the GPU to do that, only > CPU. > > GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q > -d UTILIZATION -l 3" if your'e using any recent drivers. > > > Thanks, > *Leo Souza* > > On 06/13/2011 02:44 PM, Douglas N Greve wrote: >> 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
