Re: [Freesurfer] Specification of computer

Hi Aziz -openmp 4 will speed up the recon of a single subject. If you had 16 processors and enough RAM you could run 4 subjects at the same time that way and each of them would be faster. We've had recons complete in 2-3 hours this way, depending on the anatomy. cheers Bruce On Sat, 4 Feb

Re: [Freesurfer] Specification of computer

Hi Bruce, So, I am not sure if I understand correct. Suppose, I would like to run 4 subjects simultenously, I have to run the recon-all command of each subject on each terminal with -openmp. Otherwise, is there any other options to run 4 subjects in one terminal. Thank you, Aziz. On Sat, Feb 4,

Re: [Freesurfer] Specification of computer

yes it does, and it should significantly reduce execution time unless you don't have multiple cores cheers Bruce On Sat, 4 Feb 2017, Aziz Nanthaamornphong wrote: Hi Bruce, Does FS6 support the 'openmp 8' flag? I tried to use this flag with 'recon-all -all' on FS6, but it took longer time

Re: [Freesurfer] Specification of computer

Hi Bruce, Does FS6 support the 'openmp 8' flag? I tried to use this flag with 'recon-all -all' on FS6, but it took longer time for only one subject. Thank you, Aziz. On Fri, Feb 3, 2017 at 10:16 PM, Bruce Fischl wrote: > Hi Aziz > > with multiple course you can

Re: [Freesurfer] Fwd: Regarding: mris_label2annot

Thanks Dr Kim, the cp -r command worked beautifully and I got the annotation file now. However, the permission error I tried to fix earlier too but, I still get the same permission denied error. Thanks much for your help. Kind regards, Sampada On Sat, Feb 4, 2017 at 3:39 PM, Seung-Goo KIM

Re: [Freesurfer] Fwd: Regarding: mris_label2annot

Hi Sam, It seems that you should change the permission of "Users/Sampada/Desktop/AD/fsaverage/label/“ as 755: > chmod $DIR 755 If you cannot do this because you are not the owner of the directory, then just copy fsaverage directory into your working directory: > cp -r ${SUBJECTS_DIR}/fsaverage