> Date: Fri, 16 Sep 2011 08:38:55 -0400
> From: fischl@nmr.mgh.harvard.edu
> To: Khoa@nmr.mgh.harvard.edu
> CC: sita@nmr.mgh.harvard.edu; jennifer_g_goldman@rush.edu; vy_dinh@rush.edu; freesurfer@nmr.mgh.harvard.edu; mj_coming@hotmail.com
> Subject: Re: [Freesurfer] manual editting problem
>
> p.s. you also have topological defects there, which you can tell as the
> orig (green) surface doesn't follow the voxels in the wm.mgz. The
> interventions Khoa suggests should help this as well. If you are missing
> that much wm you probably want to use control points.
>
> cheers
> Bruce
>
>
>
> On Thu, 15 Sep 2011, Khoa@nmr.mgh.harvard.edu
> wrote:
>
> > Hi Jing,
> >
> > You have some white matter voxels missing in the wm.mgz for the rh. You
> > can add some wm to that volume using the edit tool or you can also try
> > control points. If you are adding wm, make sure you select the aux volume
> > on the brush info toolbox. Fill in wm voxels for all slices. Control
> > points would help with extending the pial surf on the lh.
> >
> > -Khoa
> >
> >>
> >> Hi Bruce and Sita:
> >>
> >> Thanks for your relay. And Here are the images.
> >>
> >> Jing
> >>
> >>
> >>
> >> From: Jing Ming [mj_coming@hotmail.com]
> >>
> >> Sent: Thursday, September 15, 2011 7:31 PM
> >>
> >> To: Vy Dinh
> >>
> >> Subject: FW: [Freesurfer] manual editting problem
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>> CC: mj_coming@hotmail.com; jennifer_g_goldman@rush.edu; vydinh@rush.edu;
> >>> freesurfer@nmr.mgh.harvard.edu
> >>
> >>> From: fischl@nmr.mgh.harvard.edu
> >>
> >>> Subject: Re: [Freesurfer] manual editting problem
> >>
> >>> Date: Thu, 15 Sep 2011 20:07:41 -0400
> >>
> >>> To: sita@nmr.mgh.harvard.edu
> >>
> >>>
> >>
> >>> Can you send an image?
> >>
> >>>
> >>
> >>>
> >>
> >>>
> >>
> >>> On Sep 15, 2011, at 6:38 PM, Sita Kakunoori <sita@nmr.mgh.harvard.edu>
> >>> wrote:
> >>
> >>>
> >>
> >>>>
> >>
> >>>> How does the wm.mgz look. Correcting the white surface will correct
> >>> the
> >>
> >>>> pial surface as well.
> >>
> >>>>
> >>
> >>>> Sita.
> >>
> >>>>
> >>
> >>>>
> >>
> >>>> On Thu, 15 Sep 2011, Jing Ming wrote:
> >>
> >>>>
> >>
> >>>>>
> >>
> >>>>> Hi Surfers:
> >>
> >>>>> We have been coming
> >>
> >>>>> across several gray matter regions that are not included within the
> >>> pial
> >>
> >>>>> surface (red line) when it should be (e.g., very anterior parts of
> >>> the
> >>
> >>>>> temporal lobe). From my understanding of similar posts on the forum,
> >>> it
> >>
> >>>>> seems that there isn't a way to add this region to the pial surface
> >>> so
> >>
> >>>>> that the missing brain matter is included. We have tried using the
> >>> clone
> >>
> >>>>> tool to fill in this region, as per the tutorial and have
> >>> experimented
> >>
> >>>>> with this tool using the tutorial data. I followed the steps in the
> >>
> >>>>> tutorial but could not observe any changes when the middle button was
> >>
> >>>>> selected. Does anyone have any ideas on how to troubleshoot this
> >>
> >>>>> issue? Can someone please explain to me why this is not possible?
> >>> Also
> >>
> >>>>> how does Freesurfer determine what regions to include within the pial
> >>
> >>>>> surface? If there is a way that has been developed recently, please
> >>
> >>>>> enlighten me.
> >>
> >>>>>
> >>
> >>>>> -Jing
> >>
> >>>> _______________________________________________
> >>
> >>>> Freesurfer mailing list
> >>
> >>>> Freesurfer@nmr.mgh.harvard.edu
> >>
> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>>>
> >>
> >>>>
> >>
> >>>
> >>
> >>>
> >>
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> >>
> >>
> >>
> >>
> >>
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