External Email - Use Caution Dear Falk,
Thank you very much for your email and explanation. It is working now. I wonder how I could set the smoothing for autorecon3 as to run recon -all -all I had the options: -qcache -openmp 8 Kind regards, Rosalia On Fri, Oct 19, 2018 at 2:06 PM Falk Lüsebrink <falk.luesebr...@ovgu.de> wrote: > External Email - Use Caution > > Dear Rosalina, > > > > you should run recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 > -autorecon2 and everything will run nicely. You should not include the -i > flag again if you want to continue processing your data, as this flag tells > FreeSurfer to create a new subject folder (which already exists and > therefore give an error). > > > > Best, > > Falk > > > > > > *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta > Aguayo > *Gesendet:* Freitag, 19. Oktober 2018 11:11 > *An:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Betreff:* [Freesurfer] Problems to run -autorecon2 > > > > * External Email - Use Caution * > > Dear FreeSurfer team, > > > > I am trying to run recon -all -autorecon2 using the following command > line: *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i > /home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2* > > > > It is the same command I used yesterday to run -autorecon1 without > problems. However, maybe now it is different. Should I point to another sub > folder? I do not know which -i I should point out now. My directory for > this subject is as follows: > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ > ls > brainmask.auto.mgz nu.mgz rawavg.mgz > brainmask.mgz orig T1.mgz > mri_nu_correct.mni.log orig.mgz talairach_with_skull.log > mri_nu_correct.mni.log.bak orig_nu.mgz transforms > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ > > Best regards, > > Rosalia > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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