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
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 sg.kang422@gmail.com 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
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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-much@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 sg.kang422@gmail.com 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 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.
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 sg.kang422@gmail.com 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&type=zerocontent&guid=a9fadef6-6c 71-43eb-bd31-0c372e27c0d6] 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.
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&type=zerocontent&guid=a9fadef6-6c 71-43eb-bd31-0c372e27c0d6] ᐧ
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Seung Gul Kang -
Trisanna Sprung-Much