Hi Frank
in Linux you would just add an & to the end of the recon-all command line
to put it in the background and start however many you want. Or you can
run them from different terminal windows. If you have a lot to get
through you can do something like (note this is not debugged!):
set maxrunning=8
foreach s ($SUBJECTS)
set cmd = (recon-all -s $s ...)
set running = (`ps -aux | grep recon-all | wc -l`)
while ($running >= $maxrunning)
sleep 600
set running = (`ps -aux | grep recon-all | wc -l`)
end
eval $cmd&
end
that is csh code. Bash would be similar but not seem modifications
cheers
Bruce
On Sat, 4
Jan 2020, Frank Chau wrote:
External Email - Use Caution
Dear Bruce,
No, I want to run recon-all on 4-8 subjects at the same time. I could find
detail tutorial on the Mac platform (Run: "ls *.nii | parallel --jobs
4 recon-all -s {.} -i {} -all -qcache", after installing Xcode and
Homebrew.) But I couldn't find any similar information on the Linux
platform.
Regards
Frank
On Jan 3, 2020 11:15 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Frank
do you mean completing a single recon faster? The easiest way to
do that
is to use the -openmp <N> flag, and set <N> to the number of
threads/cores you want to use. Alternatively if you have enough
RAM you
can just run multiple recon-alls at the same time (which will
give you a
bigger effective speed increase)
cheers
Bruce
On Fri, 3 Jan 2020, Frank Chau wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
>
> May I know how to run Recon-all in parallel on Linux? I have
read some
> source said that can use "gnu parallel" to complete it. But
they do not
> describe it in detail how to perform it.
>
>
> Regards
>
>
> Frank
>
> ---------------------------
>
> FRANK C Y CHAU
>
>
> Research assistant
>
> Division of Neurology
>
> Department of Medicine
>
>
> Tel: +852 6340 2553
>
> Fax: 2872 5828
>
>
> E-mail : cyfr...@hku.hk
>
>
>
> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102
Pokfulam Road,
> Hong Kong
>
>
>
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