yep that's a typo. sorry! On Apr 25, 2011, at 9:22 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
> yes, I think that's a typo and should be autorecon2. Perhaps Nick can > confirm? > > On Mon, 25 Apr 2011, > Xiaoying Tang wrote: > >> Hi All,I find the following content on the wikipage of freesurfer: >> >> Q. I have already skull-stripped data. Can I submit it to recon-all? >> >> A: If your skull-stripped volume does not have the cerebellum, then no. If >> it does, then yes, however you will have to run the data a bit differently. >> >> First you must run only -autorecon1 like this: >> *recon-all -autorecon1 -noskullstrip -s <subjid>* >> Then you will have to make a symbolic link or copy T1.mgz to >> brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. >> Finally, open this brainmask.mgz file and check that it looks okay (there is >> no skull, cerebellum is intact; use the sample subject *bert* that comes >> with your FreeSurfer installation to make sure it looks comparable). From >> there you can run the final stages of recon-all: >> *recon-all -autrecon1 -autorecon3 -s <subjid> >> >> >> I am a little confused: should the final stages be "recon-all -autorecon2 >> -autorecon3 -s **<subjid>" since we have already run the -autorecon1 >> via **"recon-all >> -autorecon1 -noskullstrip -s <subjid>"? >> >> Thanks a lot for your answering. >> >> Best, >> Xiaoying Tang* >> > _______________________________________________ > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
