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 <rspriti@nmr.mgh.harvard.edu 
<mailto:rspriti@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
    >
    >
    >



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