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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.luesebrink@ovgu.de wrote:
External Email - Use CautionDear 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-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@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
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