Re: [Freesurfer] Most effective way to compute stats/aseg.stats
External Email - Use Caution In this case, maybe it’s possible to speed up the process a little (without loosing much in accuracy) with some parameter configuration for mri_ca_register ? I’ve checked the help for it. Only some arguments have description, but from the ones the have I can assume that at least tweaking -tol (convergence of registration) and -level (defines how many surrounding voxels will be used in interpolations) should have some positive effect on computation time. Maybe there is more? Thanks you, Aleksandr. >Воскресенье, 19 апреля 2020, 19:26 +03:00 от Bruce Fischl >: > >yes, careg is required. In general you should run things all the way to >the end of recon-all as the surfaces are used to improve the accuracy of >the aseg. > >cheers >Bruce >On Sun, 19 Apr 2020, Ерохин Александр wrote: > >> >> External Email - Use Caution >> >> Hello together, >> >> Could you please suggest the most effective way (in terms of time) for >> computation of statistics on segmented volumes from .nii source file? >> >> So far I went though the following steps: >> >> recon-all -autorecon1 -no-isrunning -subjid test >> recon-all -gcareg -no-isrunning -subjid test >> recon-all -canorm -no-isrunning -subjid test >> >> And seem to be stuck on -careg as transforms/talairach.m3z is needed to >> proceed. >> >> As far as I can tell — there is no way around recon-all -careg which seems >> to be the most time consuming in the chain of invocations based on Step-wise >> Directives (https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all). >> >> But I might be wrong and hoping for your expertise here. >> >> Many thanks, >> Aleksandr Erokhin. >> >> >___ >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] Most effective way to compute stats/aseg.stats
External Email - Use Caution Hello together, Could you please suggest the most effective way (in terms of time) for computation of statistics on segmented volumes from .nii source file? So far I went though the following steps: recon-all -autorecon1 -no-isrunning -subjid test recon-all -gcareg -no-isrunning -subjid test recon-all -canorm -no-isrunning -subjid test And seem to be stuck on -careg as transforms/talairach.m3z is needed to proceed. As far as I can tell — there is no way around recon-all -careg which seems to be the most time consuming in the chain of invocations based on Step-wise Directives ( https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all). But I might be wrong and hoping for your expertise here. Many thanks, Aleksandr Erokhin.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Most effective way to compute stats/aseg.stats
yes, careg is required. In general you should run things all the way to the end of recon-all as the surfaces are used to improve the accuracy of the aseg. cheers Bruce On Sun, 19 Apr 2020, Ерохин Александр wrote: External Email - Use Caution Hello together, Could you please suggest the most effective way (in terms of time) for computation of statistics on segmented volumes from .nii source file? So far I went though the following steps: recon-all -autorecon1 -no-isrunning -subjid test recon-all -gcareg -no-isrunning -subjid test recon-all -canorm -no-isrunning -subjid test And seem to be stuck on -careg as transforms/talairach.m3z is needed to proceed. As far as I can tell — there is no way around recon-all -careg which seems to be the most time consuming in the chain of invocations based on Step-wise Directives (https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all). But I might be wrong and hoping for your expertise here. Many thanks, Aleksandr Erokhin. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
