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Dear FreeSurfer Support,
I have a question about the run time on FreeSurfer version 7.1.1. I have been processing scans with recon-all that have been completing in as short of a time as 4.782 hours. My PI was a little worried about how short of a runtime this is as previous processing of scans (maybe of more atrophied brains) have historically taken much longer, up to a day, for all the processing steps of recon-all. Is 4.782 hours a normal runtime for recon-all on FS 7.1.1? I have also attached the log for this job that took 4.782 hours in case this helps, as I do not know enough about all the steps of recon-all to ensure that everything ran correctly. I use open science grid to run multiple jobs so if this format does not work to view the log, please let me know.
Thank you for your time and assistance.
All my best, Joanna
I don't think it is unusual; my experience is the 7.X usually takes about 6 hours, so I'm surprised by the "a day" run times. I noticed that mri_ca_register only took 1.6 hours on this case, which is pretty short. This step has poor caching performance which can be exacerbated when many are running at the same time. So maybe you did not have a lot of other recon-alls running at the time you ran this one?
On 6/1/2022 2:28 PM, Joanna L Eckhardt wrote:
External Email - Use Caution
Dear FreeSurfer Support,
I have a question about the run time on FreeSurfer version 7.1.1. I have been processing scans with recon-all that have been completing in as short of a time as 4.782 hours. My PI was a little worried about how short of a runtime this is as previous processing of scans (maybe of more atrophied brains) have historically taken much longer, up to a day, for all the processing steps of recon-all. Is 4.782 hours a normal runtime for recon-all on FS 7.1.1? I have also attached the log for this job that took 4.782 hours in case this helps, as I do not know enough about all the steps of recon-all to ensure that everything ran correctly. I use open science grid to run multiple jobs so if this format does not work to view the log, please let me know.
Thank you for your time and assistance.
All my best, Joanna
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear FreeSurfer Team,
That is good to hear! The short runtime with mri_ca_register makes sense because I submit my jobs to Open science grid where they send each job to a different core, so each scan is processed separately.
Thank you very much for your assistance.
All my best, Joanna ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, June 3, 2022 10:01 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all Runtime
I don't think it is unusual; my experience is the 7.X usually takes about 6 hours, so I'm surprised by the "a day" run times. I noticed that mri_ca_register only took 1.6 hours on this case, which is pretty short. This step has poor caching performance which can be exacerbated when many are running at the same time. So maybe you did not have a lot of other recon-alls running at the time you ran this one?
On 6/1/2022 2:28 PM, Joanna L Eckhardt wrote:
External Email - Use Caution
Dear FreeSurfer Support,
I have a question about the run time on FreeSurfer version 7.1.1. I have been processing scans with recon-all that have been completing in as short of a time as 4.782 hours. My PI was a little worried about how short of a runtime this is as previous processing of scans (maybe of more atrophied brains) have historically taken much longer, up to a day, for all the processing steps of recon-all. Is 4.782 hours a normal runtime for recon-all on FS 7.1.1? I have also attached the log for this job that took 4.782 hours in case this helps, as I do not know enough about all the steps of recon-all to ensure that everything ran correctly. I use open science grid to run multiple jobs so if this format does not work to view the log, please let me know.
Thank you for your time and assistance.
All my best, Joanna
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Joanna L Eckhardt