Hello Bruce, Yes, that is my end goal. I have a patient i edited the aseg to include left-cerebral white matter and also, want to normalize the intensity using expert option. Where should I place the "-canorm-usecps" flag ? After the command like " recon-all -autorecon2 -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time -canorm-usecps" or before autorecon2 like "recon-all -autorecon2 -canorm-usecps -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T time. Thank you.
Best, Paul On Thu, Sep 14, 2017 at 3:17 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > do you want the control points to be applied to the aseg? If so, you need > to also specify -canorm-usecps > > > cheers > Bruce > On Thu, 14 Sep 2017, miracle ozzoude wrote: > > Thanks Bruce. Yes, I want to regenerate the aseg and also use the expert >> option for control point. >> That's recon-all -autorecon2 -autorecon3 -expert -parallel -openmp 8 >> -bigventricles -3T time. >> Best, >> Paul >> >> On Thu, Sep 14, 2017 at 2:48 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> do you want it to regenerate the aseg? If not, then a). If so, then >> you would just run >> autorecon2 (instead of autorecon2-cp) >> >> cheers >> Bruce >> On Thu, 14 Sep 2017, miracle ozzoude wrote: >> >> I used the expert option for control points and manually >> edited the >> aseg.presurf.mgz. Which is the >> proper flag to use in other to incorporate the respective >> changes? >> a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3 >> -expert -parallel >> -openmp 8 >> -bigventricles -3T -time >> >> or >> >> b) recon-all -autorecon2-cp -autorecon3 -expert -parallel >> -openmp 8 >> -bigventricles -3T -time >> >> Thanks. >> >> Best, >> Paul >> >> >> >> _______________________________________________ >> 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. >> >> >> >> > _______________________________________________ > 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. > >
_______________________________________________ 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.
