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I ran 38 subjects through Freesurfer 6.0 on a supercomputer here at Washu. The super computer is about 3 years old. Of those 38 subjects, 7 exceeded 20 hour time limit on the batch script. The others took about 12 hours to finish. All subjects had a 1mm isotropic MPRAGE and FLAIR. Below is the command I used for one of them. Is there a reason for some subjects recon-all would take more then 20 hours?
recon-all -s 100000016_20170414 -i /scratch/brierm/Images/100000016_20170414_T1.nii -FLAIR /scratch/brierm/Images/100000016_20170414_FLAIR.nii -FLAIRpial -all -mprage -hippocampal-subfields-T1 -qcache
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Hi Aaron,
I think there are time stamps in the log file, so you should be able to see what part of the pipeline took so long.
If you still have one of the log files, could you attach it?
Best,
Tim
On June 13, 2019 at 6:23 PM Aaron Tanenbaum aaron.b.tanenbaum@gmail.com wrote:
External Email - Use CautionI ran 38 subjects through Freesurfer 6.0 on a supercomputer here at Washu. The super computer is about 3 years old. Of those 38 subjects, 7 exceeded 20 hour time limit on the batch script. The others took about 12 hours to finish. All subjects had a 1mm isotropic MPRAGE and FLAIR. Below is the command I used for one of them. Is there a reason for some subjects recon-all would take more then 20 hours?
recon-all -s 100000016_20170414 -i /scratch/brierm/Images/100000016_20170414_T1.nii -FLAIR /scratch/brierm/Images/100000016_20170414_FLAIR.nii -FLAIRpial -all -mprage -hippocampal-subfields-T1 -qcache _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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Most likely some subjects had more topology errors that required correcting.
Matt.
On 6/13/19, 12:05 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ts+ml@rcmd.org> wrote:
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Hi Aaron,
I think there are time stamps in the log file, so you should be able to see what part of the pipeline took so long.
If you still have one of the log files, could you attach it?
Best,
Tim
> On June 13, 2019 at 6:23 PM Aaron Tanenbaum aaron.b.tanenbaum@gmail.com wrote: > > > External Email - Use Caution > > I ran 38 subjects through Freesurfer 6.0 on a supercomputer here at Washu. > The super computer is about 3 years old. Of those 38 subjects, 7 exceeded > 20 hour time limit on the batch script. The others took about 12 hours to > finish. All subjects had a 1mm isotropic MPRAGE and FLAIR. Below is the > command I used for one of them. Is there a reason for some subjects > recon-all would take more then 20 hours? > > > recon-all -s 100000016_20170414 -i > /scratch/brierm/Images/100000016_20170414_T1.nii -FLAIR > /scratch/brierm/Images/100000016_20170414_FLAIR.nii -FLAIRpial -all > -mprage -hippocampal-subfields-T1 -qcache > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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