Hi John

so, you don't want to give recon-all multiple subjects. If you have enough ram you should just call it once for each subject and not use the openmp flag

cheers Bruce On Thu, 19 Jul 2018, John Absher wrote:

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We are trying to run many subjects through recon-all in batches on an 8 core Windows Server on which we have virtualBox running CentOS7 and freesurfer 6.

Can you tell me if this command will utilize all 8 cores effectively to process all 8 subjects simultaneously?

recon-all -subjid TBI1_002 -i TBI1_002_v1.nii.gz \

-subjid TBI1_003 –i  TBI1_003_v1.nii.gz \

-subjid TBI1_005 -i TBI1_005_v1.nii.gz \

-subjid TBI1_006 -i TBI1_006_v1.nii.gz \

-subjid TBI1_007 -i TBI1_007_v1.nii.gz \

-subjid TBI1_009 -i TBI1_009_v1.nii.gz \

-subjid TBI1_012 -i TBI1_012_v1.nii.gz \

-subjid TBI1_013 -i TBI1_013_v1.nii.gz \

-all -parallel -openmp 8

Thanks,

John

John R. Absher, MD, FAAN

GHS Neurosciences

jabsher@ghs.org

864-350-6655 (mobile)