External Email - Use Caution 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 >>> >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
