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Dear Tim,

Sorry, I am a Linux code beginner. I installed the GNU parallel in my Linux. 
May I know how to adapt the script of “ run_reconall_parallel_wrapper.bash” to 
my own need? Thank you.

Regards

Frank

> On Jan 4, 2020, at 6:12 PM, Tim Schäfer <ts...@rcmd.org> wrote:
> 
>        External Email - Use Caution        
> 
> Hi Frank,
> 
> The OS shouldn't make any difference as long as you use the same shell. You 
> will have to install GNU parallel first as it's usually not installed by 
> default under Linux (on Debian-based distros: `sudo apt-get install 
> parallel`).
> 
> I have shell scripts for the BASH shell here if you want: 
> 
>   
> https://github.com/dfsp-spirit/shell-tools/tree/master/gnu_parallel_reconall_minimal
> 
> If you need an explanation, you can read this before using them:
> 
>   
> https://www.xsmd.org/brain/2019/03/13/using-gnu-parallel-to-speedup-neuroimaging/
> 
> Best,
> 
> Tim
> 
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> 
>> On January 4, 2020 at 7:08 AM Frank Chau <cyfr...@hku.hk> 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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