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
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.
> >
> >
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.
> >
> >
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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.
