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
