External Email - Use Caution Dear Falk,
I understand. I will do exactly the same for all the participants. Thank you very much for all your helpful and kind explanations. Best regards, Rosalia On Fri, Oct 19, 2018 at 3:13 PM Falk Lüsebrink <falk.luesebr...@ovgu.de> wrote: > External Email - Use Caution > > Dear Rosalia, > > > > When you use the openmp flag, you should make sure to use it always in the > same for all subjects in your study, as otherwise you may introduce a bias > (in your case either use it for autorecon1, autorecon2, and autorecon3 or > use it for autorecon2 and autorecon3 only). With regards to the qcache > flag, it is of no concern, as it does not affect anything in autorecon1 (as > far as I know). > > > > 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 14:40 > *An:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] Problems to run -autorecon2 > > > > * External Email - Use Caution * > > Dear Falk, > > > > Thank you very much. > > Once last question: what would happen if I did run -autorecon1 without the > flags: *-qcache -openmp 8’ *and I use them in autorecon2 or 3? > > > > Best regards, > > Rosalia > > > > On Fri, Oct 19, 2018 at 2:34 PM Falk Lüsebrink <falk.luesebr...@ovgu.de> > wrote: > > * External Email - Use Caution * > > Dear Rosalia, > > > > You can specify all flags in every call of recon-all. If this flags does > not change any commands, they will simply be ignored. > > > > In your case, to first run autorecon1, overwrite the brainmask and > continue with autorecon2 and 3, you can do the following: > > 1. Run ‘recon-all -autorecon1 -i <your input> -s <your subject ID> > -qcache -openmp 8’ > > 2. Delete brainmaskmgz and use your brain mask created in BET with > mri_mask on the T1.mgz and name the output brainmask.mgz > > 3. Run ‘recon-all -autorecon2 -autorecon3 -s <your subject ID> > -qcache -openmp 8’ > > > > > > 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 14:10 > *An:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] Problems to run -autorecon2 > > > > * 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 > > _______________________________________________ > 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
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