Re: [Freesurfer] pial edits in subject with severe atrophy

[Corinna Bauer]

Hi Bruce,
I exported the ribbon.mgz to itksnap and was able to edit the grey matter
to include the atrophic frontal areas. I am wondering if there is a way to
have these edits reflected in the pial surface?

Thanks.

Corinna

On Wed, Feb 10, 2016 at 4:02 PM, Corinna Bauer  wrote:

> ok thanks.
>
> On Wed, Feb 10, 2016 at 3:40 PM, Bruce Fischl 
> wrote:
>
>> not to my knowledge, but others may have developed something
>> Bruce
>> On Wed, 10 Feb
>> 2016, Corinna Bauer wrote:
>>
>> > Thanks, Bruce.
>> > In an earlier thread from '09 with a similar problem(
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html
>> > ), it was mentioned that there was a method being developed to edit the
>> > surface mesh. Is that option still available and would it help? Since
>> this
>> > step in our analysis stream is central to everything else, we are
>> willing to
>> > try whatever it takes.
>> >
>> > Corinna
>> >
>> > On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> > wrote:
>> >   Sorry Corinna
>> >
>> >   I meant to answer this the first time but it slipped through the
>> >   cracks.
>> >   I doubt there is much you can do if there is that big a lesion.
>> >   If the
>> >   topology is wrong and you can't see tissue in those regions it's
>> >   going to
>> >   be very hard
>> >   Bruce
>> >
>> >
>> >   On Wed, 10 Feb 2016,
>> >   Corinna Bauer wrote:
>> >
>> >   > Dear Experts,
>> >   >
>> >   > I have a subject with severe atrophy in bilateral frontal and
>> >   parietal
>> >   > regions and after many rounds of edits to the brainmask,
>> >   wm.mgz, and control
>> >   > points, these regions are still left uncaptured. Is there a
>> >   way to edit the
>> >   > pial surface to include these grey matter regions? I am
>> >   hesitant to draw
>> >   > them in via the wm surface since there is no definite WM
>> >   present.
>> >   >
>> >   > I do have a FLAIR also on this subject.
>> >   >
>> >   > I've attached a couple examples.
>> >   >
>> >   > Thanks!
>> >   >
>> >   > Corinna
>> >   >
>> >   >
>> > ___
>> > 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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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
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Re: [Freesurfer] pial edits in subject with severe atrophy

[Bruce Fischl]

Sorry Corinna

I meant to answer this the first time but it slipped through the cracks. 
I doubt there is much you can do if there is that big a lesion. If the 
topology is wrong and you can't see tissue in those regions it's going to 
be very hard
Bruce


On Wed, 10 Feb 2016, 
Corinna Bauer wrote:

> Dear Experts,
> 
> I have a subject with severe atrophy in bilateral frontal and parietal
> regions and after many rounds of edits to the brainmask, wm.mgz, and control
> points, these regions are still left uncaptured. Is there a way to edit the
> pial surface to include these grey matter regions? I am hesitant to draw
> them in via the wm surface since there is no definite WM present.
> 
> I do have a FLAIR also on this subject.
> 
> I've attached a couple examples.
> 
> Thanks!
> 
> Corinna
> 
>
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[Freesurfer] pial edits in subject with severe atrophy

[Corinna Bauer]

Dear Experts,

I have a subject with severe atrophy in bilateral frontal and parietal
regions and after many rounds of edits to the brainmask, wm.mgz, and
control points, these regions are still left uncaptured. Is there a way to
edit the pial surface to include these grey matter regions? I am hesitant
to draw them in via the wm surface since there is no definite WM present.

I do have a FLAIR also on this subject.

I've attached a couple examples.

Thanks!

Corinna
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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
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Re: [Freesurfer] pial edits in subject with severe atrophy

[Corinna Bauer]

I should mention that the aseg file captures the GM outside the pial
surface.

On Wed, Feb 10, 2016 at 1:23 PM, Corinna Bauer  wrote:

> Thanks, Bruce.
> In an earlier thread from '09 with a similar problem (
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html),
> it was mentioned that there was a method being developed to edit the
> surface mesh. Is that option still available and would it help? Since this
> step in our analysis stream is central to everything else, we are willing
> to try whatever it takes.
>
> Corinna
>
> On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl  > wrote:
>
>> Sorry Corinna
>>
>> I meant to answer this the first time but it slipped through the cracks.
>> I doubt there is much you can do if there is that big a lesion. If the
>> topology is wrong and you can't see tissue in those regions it's going to
>> be very hard
>> Bruce
>>
>>
>> On Wed, 10 Feb 2016,
>> Corinna Bauer wrote:
>>
>> > Dear Experts,
>> >
>> > I have a subject with severe atrophy in bilateral frontal and parietal
>> > regions and after many rounds of edits to the brainmask, wm.mgz, and
>> control
>> > points, these regions are still left uncaptured. Is there a way to edit
>> the
>> > pial surface to include these grey matter regions? I am hesitant to draw
>> > them in via the wm surface since there is no definite WM present.
>> >
>> > I do have a FLAIR also on this subject.
>> >
>> > I've attached a couple examples.
>> >
>> > Thanks!
>> >
>> > Corinna
>> >
>> >
>> ___
>> 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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Re: [Freesurfer] pial edits in subject with severe atrophy

[Corinna Bauer]

ok thanks.

On Wed, Feb 10, 2016 at 3:40 PM, Bruce Fischl 
wrote:

> not to my knowledge, but others may have developed something
> Bruce
> On Wed, 10 Feb
> 2016, Corinna Bauer wrote:
>
> > Thanks, Bruce.
> > In an earlier thread from '09 with a similar problem(
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html
> > ), it was mentioned that there was a method being developed to edit the
> > surface mesh. Is that option still available and would it help? Since
> this
> > step in our analysis stream is central to everything else, we are
> willing to
> > try whatever it takes.
> >
> > Corinna
> >
> > On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >   Sorry Corinna
> >
> >   I meant to answer this the first time but it slipped through the
> >   cracks.
> >   I doubt there is much you can do if there is that big a lesion.
> >   If the
> >   topology is wrong and you can't see tissue in those regions it's
> >   going to
> >   be very hard
> >   Bruce
> >
> >
> >   On Wed, 10 Feb 2016,
> >   Corinna Bauer wrote:
> >
> >   > Dear Experts,
> >   >
> >   > I have a subject with severe atrophy in bilateral frontal and
> >   parietal
> >   > regions and after many rounds of edits to the brainmask,
> >   wm.mgz, and control
> >   > points, these regions are still left uncaptured. Is there a
> >   way to edit the
> >   > pial surface to include these grey matter regions? I am
> >   hesitant to draw
> >   > them in via the wm surface since there is no definite WM
> >   present.
> >   >
> >   > I do have a FLAIR also on this subject.
> >   >
> >   > I've attached a couple examples.
> >   >
> >   > Thanks!
> >   >
> >   > Corinna
> >   >
> >   >
> > ___
> > 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
>
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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
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Re: [Freesurfer] pial edits in subject with severe atrophy

[Bruce Fischl]

not to my knowledge, but others may have developed something
Bruce
On Wed, 10 Feb 
2016, Corinna Bauer wrote:

> Thanks, Bruce.
> In an earlier thread from '09 with a similar 
> problem(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html
> ), it was mentioned that there was a method being developed to edit the
> surface mesh. Is that option still available and would it help? Since this
> step in our analysis stream is central to everything else, we are willing to
> try whatever it takes.
> 
> Corinna
> 
> On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl 
> wrote:
>   Sorry Corinna
>
>   I meant to answer this the first time but it slipped through the
>   cracks.
>   I doubt there is much you can do if there is that big a lesion.
>   If the
>   topology is wrong and you can't see tissue in those regions it's
>   going to
>   be very hard
>   Bruce
> 
>
>   On Wed, 10 Feb 2016,
>   Corinna Bauer wrote:
>
>   > Dear Experts,
>   >
>   > I have a subject with severe atrophy in bilateral frontal and
>   parietal
>   > regions and after many rounds of edits to the brainmask,
>   wm.mgz, and control
>   > points, these regions are still left uncaptured. Is there a
>   way to edit the
>   > pial surface to include these grey matter regions? I am
>   hesitant to draw
>   > them in via the wm surface since there is no definite WM
>   present.
>   >
>   > I do have a FLAIR also on this subject.
>   >
>   > I've attached a couple examples.
>   >
>   > Thanks!
>   >
>   > Corinna
>   >
>   >
> ___
> 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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Re: [Freesurfer] pial edits in subject with severe atrophy

[Corinna Bauer]

Thanks, Bruce.
In an earlier thread from '09 with a similar problem (
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html),
it was mentioned that there was a method being developed to edit the
surface mesh. Is that option still available and would it help? Since this
step in our analysis stream is central to everything else, we are willing
to try whatever it takes.

Corinna

On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl 
wrote:

> Sorry Corinna
>
> I meant to answer this the first time but it slipped through the cracks.
> I doubt there is much you can do if there is that big a lesion. If the
> topology is wrong and you can't see tissue in those regions it's going to
> be very hard
> Bruce
>
>
> On Wed, 10 Feb 2016,
> Corinna Bauer wrote:
>
> > Dear Experts,
> >
> > I have a subject with severe atrophy in bilateral frontal and parietal
> > regions and after many rounds of edits to the brainmask, wm.mgz, and
> control
> > points, these regions are still left uncaptured. Is there a way to edit
> the
> > pial surface to include these grey matter regions? I am hesitant to draw
> > them in via the wm surface since there is no definite WM present.
> >
> > I do have a FLAIR also on this subject.
> >
> > I've attached a couple examples.
> >
> > Thanks!
> >
> > Corinna
> >
> >
> ___
> 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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