External Email - Use Caution Dear Frank,
I have updated the header of the script with much more detailed instructions. I hope they help. If not, let me know where you are stuck. Tim > On January 6, 2020 at 2:56 PM Frank Chau <cyfr...@hku.hk> wrote: > > > 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 -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
