Re: [Freesurfer] Can I change the pial surface outline by the adding the control point?

2016-09-30 Thread Bruce Fischl 
that's true, but if the white matter surface is already correct you can 
change some of the intensity bounds in mris_make_surfaces. The 
automatically calculated ones will be in the recon-all.log and you should 
check them before changing them


cheers
Bruce



On Fri, 30 Sep 2016, Trisanna 
Sprung-Much wrote:



Hi there

To my understanding, if you want to edit the pial (push it outwards more)
then you need to edit the white matter, as the pial is made from the white
matter surface. You can do this by manually extending the white matter
surface and re-running your surfaces.

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:07 PM, Seung Gul Kang 
wrote:
  Hi Freesurfer expert, 
I am doing visual editing. 
In some subjects, the pial surface border is somewhat narrow (within
the border of graymatter in my view) although there is no skull
stripping error. 
I heard that adding the control point might extend the border of
graymatter as well as that of white matter from other researcher.
Is it true?
Or, is there other way to edit to extend the pial surface border?

Thank you. 

Best,
Seung-Gul
---
Seung Gul Kang, M.D., Ph.D. 

Psychiatrist, Associate Professor; Department of Psychiatry, Gil
Medical Center, Gachon University, School of Medicine, 21,
Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
Research scholar; Sleep Disorders Clinical Research Program,
Department of Psychiatry, Massachusetts General Hospital, Harvard
Medical School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA
Collaboration researcher; Division of Sleep & Circadian Disorders,
Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave,
Boston MA 02115
[t?sender=ac2cua2FuZzQyMkBnbWFpbC5jb20%3D=zerocontent=a9fadef6-6c
71-43eb-bd31-0c372e27c0d6] ᐧ

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Re: [Freesurfer] Can I change the pial surface outline by the adding the control point?

2016-09-30 Thread Bruce Fischl 

Hi  Seung-Gul

the easiest way to get it to extend further is to play with the intenisty 
bounds in mris_make_surfaces. For example, if you reduce 
max_gray_at_the_csf_border you will force it to settle further out


cheers
Bruce
On Fri, 
30 Sep 2016, Seung Gul Kang wrote:



Hi Freesurfer expert, 
I am doing visual editing. 
In some subjects, the pial surface border is somewhat narrow (within the
border of graymatter in my view) although there is no skull stripping
error. 
I heard that adding the control point might extend the border of graymatter
as well as that of white matter from other researcher.
Is it true?
Or, is there other way to edit to extend the pial surface border?

Thank you. 

Best,
Seung-Gul
---
Seung Gul Kang, M.D., Ph.D. 

Psychiatrist, Associate Professor; Department of Psychiatry, Gil Medical
Center, Gachon University, School of Medicine, 21, Namdong-daero 774
beon-gil, Namdong-gu, Incheon, 21565, South Korea
Research scholar; Sleep Disorders Clinical Research Program, Department of
Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1
Bowdoin Square, 9th floor, Boston, MA 02114, USA
Collaboration researcher; Division of Sleep & Circadian Disorders, Brigham &
Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston MA 02115
[t?sender=ac2cua2FuZzQyMkBnbWFpbC5jb20%3D=zerocontent=a9fadef6-6c
71-43eb-bd31-0c372e27c0d6] ᐧ

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Can I change the pial surface outline by the adding the control point?

2016-09-30 Thread Seung Gul Kang 
Hi Trisanna,

Thank you for your useful and prompt answer!!

Have a great day.

Best,
Seung-Gul
ᐧ

---
*Seung Gul Kang, M.D., Ph.D. *

*Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical
Center, Gachon University, School of Medicine, 21, Namdong-daero 774
beon-gil, Namdong-gu, Incheon, 21565, South Korea
*Research scholar*; Sleep Disorders Clinical Research Program, Department
of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1
Bowdoin Square, 9th floor, Boston, MA 02114, USA
*Collaboration researcher*; Division of Sleep & Circadian Disorders,
Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave,
Boston MA 02115

2016-09-30 12:13 GMT-04:00 Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca>:

> Hi there
>
> To my understanding, if you want to edit the pial (push it outwards more)
> then you need to edit the white matter, as the pial is made from the white
> matter surface. You can do this by manually extending the white matter
> surface and re-running your surfaces.
>
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Sep 30, 2016 at 12:07 PM, Seung Gul Kang 
> wrote:
>
>> Hi Freesurfer expert,
>>
>> I am doing visual editing.
>> In some subjects, the pial surface border is somewhat narrow (within the
>> border of graymatter in my view) although there is no skull stripping
>> error.
>> I heard that adding the control point might extend the border of
>> graymatter as well as that of white matter from other researcher.
>> Is it true?
>> Or, is there other way to edit to extend the pial surface border?
>>
>> Thank you.
>>
>> Best,
>> Seung-Gul
>> ---
>> *Seung Gul Kang, M.D., Ph.D. *
>>
>> *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil
>> Medical Center, Gachon University, School of Medicine, 21, Namdong-daero
>> 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
>> *Research scholar*; Sleep Disorders Clinical Research Program,
>> Department of Psychiatry, Massachusetts General Hospital, Harvard Medical
>> School, 1 Bowdoin Square, 9th floor, Boston, MA 02114, USA
>> *Collaboration researcher*; Division of Sleep & Circadian Disorders,
>> Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave,
>> Boston MA 02115
>> ᐧ
>>
>> ___
>> 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
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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.
>
>
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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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dispose of the e-mail.

Re: [Freesurfer] Can I change the pial surface outline by the adding the control point?

2016-09-30 Thread Trisanna Sprung-Much 
Hi there

To my understanding, if you want to edit the pial (push it outwards more)
then you need to edit the white matter, as the pial is made from the white
matter surface. You can do this by manually extending the white matter
surface and re-running your surfaces.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Sep 30, 2016 at 12:07 PM, Seung Gul Kang 
wrote:

> Hi Freesurfer expert,
>
> I am doing visual editing.
> In some subjects, the pial surface border is somewhat narrow (within the
> border of graymatter in my view) although there is no skull stripping
> error.
> I heard that adding the control point might extend the border of
> graymatter as well as that of white matter from other researcher.
> Is it true?
> Or, is there other way to edit to extend the pial surface border?
>
> Thank you.
>
> Best,
> Seung-Gul
> ---
> *Seung Gul Kang, M.D., Ph.D. *
>
> *Psychiatrist, Associate Professor*; Department of Psychiatry, Gil
> Medical Center, Gachon University, School of Medicine, 21, Namdong-daero
> 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
> *Research scholar*; Sleep Disorders Clinical Research Program, Department
> of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1
> Bowdoin Square, 9th floor, Boston, MA 02114, USA
> *Collaboration researcher*; Division of Sleep & Circadian Disorders,
> Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave,
> Boston MA 02115
> ᐧ
>
> ___
> 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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Can I change the pial surface outline by the adding the control point?

2016-09-30 Thread Seung Gul Kang 
Hi Freesurfer expert,

I am doing visual editing.
In some subjects, the pial surface border is somewhat narrow (within the
border of graymatter in my view) although there is no skull stripping
error.
I heard that adding the control point might extend the border of graymatter
as well as that of white matter from other researcher.
Is it true?
Or, is there other way to edit to extend the pial surface border?

Thank you.

Best,
Seung-Gul
---
*Seung Gul Kang, M.D., Ph.D. *

*Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical
Center, Gachon University, School of Medicine, 21, Namdong-daero 774
beon-gil, Namdong-gu, Incheon, 21565, South Korea
*Research scholar*; Sleep Disorders Clinical Research Program, Department
of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1
Bowdoin Square, 9th floor, Boston, MA 02114, USA
*Collaboration researcher*; Division of Sleep & Circadian Disorders,
Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave,
Boston MA 02115
ᐧ
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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.