Dear FreeSurfer Staff,
We have conducted a brain volume study in normal Thai elderly. We found that the process time to analyze the brain of 20% of our subject took over 40 hours. The maximum process time is 99 hours. Eventhough the size of imaging file is around 20 MB and use “recon -all” command to process file.
It would be grateful if you could help to explain tedious process time of FreeSurfer and how to shorten this process time.
Our Machine spec. is as following: • INTEL i5 – 4260U CPU@1.4GHz • RAM 8 MB • Cent OS 6.x
Best Regards Ritthikrai Thaweecharoen Data Scientist Research and Development Department Tel: 02 755 1919
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Hi Ritthikrai
the amount of time depends on both how abnormal the anatomy is and how high the CNR of your scan is. If you send us some details about your acquisition we might be able to help optimize it, but otherwise you might be stuck with long running time. You can also use more than 1 thread to shorten thing with the -openmp flag to recon-all, if you have the hardware.
cheers Bruce
On Fri, 12 Jan 2018, Ritthikrai Thaweecharoen wrote:
Dear FreeSurfer Staff,
We have conducted a brain volume study in normal Thai elderly. We found that the process time to analyze the brain of 20% of our subject took over 40 hours. The maximum process time is 99 hours. Eventhough the size of imaging file is around 20 MB and use “recon -all” command to process file.
It would be grateful if you could help to explain tedious process time of FreeSurfer and how to shorten this process time.
Our Machine spec. is as following: • INTEL i5 – 4260U CPU@1.4GHz • RAM 8 MB • Cent OS 6.x
Best Regards
Ritthikrai Thaweecharoen
Data Scientist
Research and Development Department
Tel: 02 755 1919
Disclaimer: The information contained in this electronic mail message may be confidential and protected information intended only for the use of the entity name above. As the recipient of this information you may be prohibited by law from disclosing this information to any other parties without specific written authorization from the individual to whom it pertains. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any disclosure, dissemination, distribution, copying, or action taken in reliance on the contents of this communication is strictly prohibited, If you have received this communication in error, please notify me back immediately by telephone and destroy the message and its attachments.
Hi Bruce,
Thanks for your suggestion, the “-openmp” flag can shorten process time over 70%.
Ritthikrai.
On 13/1/18 03:29, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Ritthikrai
the amount of time depends on both how abnormal the anatomy is and how high the CNR of your scan is. If you send us some details about your acquisition we might be able to help optimize it, but otherwise you might be stuck with long running time. You can also use more than 1 thread to shorten thing with the -openmp flag to recon-all, if you have the hardware.
cheers Bruce
On Fri, 12 Jan 2018, Ritthikrai Thaweecharoen wrote:
> > Dear FreeSurfer Staff, > > We have conducted a brain volume study in normal Thai elderly. We found that the process time to > analyze the brain of 20% of our subject took over 40 hours. The maximum process time is 99 hours. > Eventhough the size of imaging file is around 20 MB and use “recon -all” command to process file. > > It would be grateful if you could help to explain tedious process time of FreeSurfer and how to > shorten this process time. > > > > Our Machine spec. is as following: > • INTEL i5 – 4260U CPU@1.4GHz > • RAM 8 MB > • Cent OS 6.x > > > > Best Regards > > Ritthikrai Thaweecharoen > > Data Scientist > > Research and Development Department > > Tel: 02 755 1919 > > > > > > > > Disclaimer: > The information contained in this electronic mail message may be confidential and protected > information intended only for the use of the entity name above. As the recipient of this information > you may be prohibited by law from disclosing this information to any other parties without specific > written authorization from the individual to whom it pertains. If the reader of this message is not > the intended recipient, or the employee or agent responsible for delivering it to the intended > recipient, you are hereby notified that any disclosure, dissemination, distribution, copying, or > action taken in reliance on the contents of this communication is strictly prohibited, If you have > received this communication in error, please notify me back immediately by telephone and destroy the > message and its attachments. > > >
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Bruce Fischl -
Ritthikrai Thaweecharoen