Dear Bruce, thanks for the reply. I often have the case that the aseg.mgz is already correct, however the surfaces cross because the aparc+aseg.mgz incorrectly classified the hemispheres. If running autorecon2-cp uses the aseg.mgz, which is already correct, would that make any changes to the aparc+aseg.mgz?
Cheers, Clara ----- Ursprüngliche Mail ----- Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Gesendet: Freitag, 24. April 2015 03:12:55 Betreff: Re: [Freesurfer] crossing medial surfaces I don't think you want noaseg. Why not try autorecon2-cp so it starts after the aseg but uses it? cheers Bruce On Thu, 23 Apr 2015, Clara Kuehn wrote: > Hi Paul, > > thanks for your reply. I think the problem is that after editing the aseg.mgz > and rerunning -autorecon2-noaseg it doesn't update the aparc+aseg.mgz, so the > surfaces still cross. > > Cheers, Clara > > ----- Ursprüngliche Mail ----- > Von: silve...@gmx.com > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Donnerstag, 23. April 2015 03:24:51 > Betreff: Re: [Freesurfer] crossing medial surfaces > > Hi Clara, > The method for dealing with the crossing medial surfaces that works for me is > decribed in the email below. Though, I'm not sure if there are any issues or > concerns with this approach particularly in regard to thickness or the > segmentations. > Paul > Sent: Tuesday, October 22, 2013 at 9:49 AM > From: "silve...@gmx.com" <silve...@gmx.com> > To: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] medial wall crossing the surface: repost > Thanks Bruce for your response, I'll fix aseg where it is incorrect, but what > about the instances where the aseg is correct and the pial surfaces cross? > Other than needing to update aseg.stats, are there any other concerns with > the 'hemisphere' approach I described below? > > Thanks again, > Paul > > > >> ----- Original Message ----- >> From: Bruce Fischl >> Sent: 10/22/13 09:46 AM >> To: silve...@gmx.com >> Subject: Re: [Freesurfer] medial wall crossing the surface: repost >> >> Try fixing the aseg and rerunning >> Cheers >> Bruce >> >>> On Oct 21, 2013, at 6:23 PM, "silve...@gmx.com" <silve...@gmx.com> wrote: >>> >>> Not always, but yes, in some instances the aseg crosses. >>> >>> >>>> ----- Original Message ----- >>>> From: Bruce Fischl >>>> Sent: 10/18/13 01:22 PM >>>> To: silve...@gmx.com >>>> Subject: Re: [Freesurfer] medial wall crossing the surface >>>> >>>> Does the aseg cross as well? >>>> >>>> >>>> >>>>> On Oct 17, 2013, at 10:07 PM, "silve...@gmx.com" <silve...@gmx.com> wrote: >>>>> >>>>> Dear All, >>>>> >>>>> I too am seeing the medial pial surfaces crossing hemispheres in some >>>>> subjects. >>>>> >>>>> The approach that appears to be working for me involves making copies of >>>>> brainmask.mgz and aseg.mgz >>>>> For the left hemisphere crossing into the right, edit brainmask.mgz and >>>>> aseg.mgz to delete voxels at the crossing belonging to the right >>>>> hemisphere. >>>>> I then run recon-all -autorecon-pial -hemi lh -subjid subject >>>>> followed by returning the brainmask.mgz and aseg.mgz back to their >>>>> original copy. >>>>> >>>>> This is similarly repeated for the right hemisphere crossing into the >>>>> left. >>>>> >>>>> Are there any issues or concerns with this approach particularly in >>>>> regard to thickness or the segmentations? >>>>> >>>>> Thanks, >>>>> >>>>> 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 > > > _______________________________________________ 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
