I ran one of my brains through recon-all and the skull strip and talairach were normal. When I checked the white matter edits with tkmedit, the right hemisphere wm and pial surface lines are including some of the left hemisphere, and the right temporal lobes are not included as white matter or in the pial surface. I thought it may be a tailarach problem, but it looks normal. Any suggestion on what could be wrong. I may try using control points and re-running it with <recon-all -autorecon2-cp...> Thanks!
Hi Amanda,
What are the intensity values of the regions that are being left out? If they aren't near 110 then you should definitely use some control points.
Where are the rh surfaces including some of the left hemisphere? Is it along the medial wall?
Jenni
On Wed, 24 May 2006, Amanda Dow wrote:
I ran one of my brains through recon-all and the skull strip and talairach were normal. When I checked the white matter edits with tkmedit, the right hemisphere wm and pial surface lines are including some of the left hemisphere, and the right temporal lobes are not included as white matter or in the pial surface. I thought it may be a tailarach problem, but it looks normal. Any suggestion on what could be wrong. I may try using control points and re-running it with <recon-all -autorecon2-cp...> Thanks!
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This sounds like a bug we were having on certain platforms. Nick?
Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Alex,
which freesurfer release are you using?
Nick
On Thu, 2006-05-25 at 17:59 -0400, Doug Greve wrote:
This sounds like a bug we were having on certain platforms. Nick?
Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm running
$Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $
On Debian.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 7:59 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
This sounds like a bug we were having on certain platforms. Nick?
Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
which curvature values. Can you send the output?
On Fri, 26 May 2006, Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I mainly interested in the mean curvature.
This is output for a gyral ROI:
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 395 1297 3.145 0.780 0.151 0.027 4.123 0.572
This is for a sulcal ROI;
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 563 1693 2.992 0.567 0.121 0.068 48.616 4.783
Cheers, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
which curvature values. Can you send the output?
On Fri, 26 May 2006, Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote:
I mainly interested in the mean curvature.
This is output for a gyral ROI:
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 395 1297 3.145 0.780 0.151 0.027 4.123 0.572
This is for a sulcal ROI;
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 563 1693 2.992 0.567 0.121 0.068 48.616 4.783
Cheers, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
which curvature values. Can you send the output?
On Fri, 26 May 2006, Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yup. That looks fine.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote:
I mainly interested in the mean curvature.
This is output for a gyral ROI:
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 395 1297 3.145 0.780 0.151 0.027 4.123 0.572
This is for a sulcal ROI;
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 563 1693 2.992 0.567 0.121 0.068 48.616 4.783
Cheers, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
which curvature values. Can you send the output?
On Fri, 26 May 2006, Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
and if you click on the gyri do you get negative values? On Fri, 26 May 2006, Fornito, Alexander wrote:
Yup. That looks fine.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote:
I mainly interested in the mean curvature.
This is output for a gyral ROI:
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 395 1297 3.145 0.780 0.151 0.027 4.123 0.572
This is for a sulcal ROI;
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 563 1693 2.992 0.567 0.121 0.068 48.616 4.783
Cheers, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
which curvature values. Can you send the output?
On Fri, 26 May 2006, Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
p.s. sorry, the mean and Gaussian curvatures displayed in mris_anatomical_stats are absolute value. I forgot this, sorry. The integrate Gaussian curvature is actually a topological invariant, so doesn't tell you much about the surface. Do you really need signed mean curvaature averaged over a region? If so, you could specify -T curv, so that the "thickness" is actually the curvature, and it will give you the mean and std.
Bruce
On Fri, 26 May 2006, Fornito, Alexander wrote:
Yup. That looks fine.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote:
I mainly interested in the mean curvature.
This is output for a gyral ROI:
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 395 1297 3.145 0.780 0.151 0.027 4.123 0.572
This is for a sulcal ROI;
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 563 1693 2.992 0.567 0.121 0.068 48.616 4.783
Cheers, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
which curvature values. Can you send the output?
On Fri, 26 May 2006, Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
No, I don't need signed values necessarily. So just to double-check then, higher mean curvature for averaged across a gyral ROI label would mean the gyrus has a more steeply peaked appearance, whereas high values for a sulcal label would, conversely, mean the sulcus resembles a shraply bended valley?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 10:21 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
p.s. sorry, the mean and Gaussian curvatures displayed in mris_anatomical_stats are absolute value. I forgot this, sorry. The integrate Gaussian curvature is actually a topological invariant, so doesn't tell you much about the surface. Do you really need signed mean curvaature averaged over a region? If so, you could specify -T curv, so that the "thickness" is actually the curvature, and it will give you the mean and std.
Bruce
On Fri, 26 May 2006, Fornito, Alexander wrote:
Yup. That looks fine.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote:
I mainly interested in the mean curvature.
This is output for a gyral ROI:
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 395 1297 3.145 0.780 0.151 0.027 4.123 0.572
This is for a sulcal ROI;
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 563 1693 2.992 0.567 0.121 0.068 48.616 4.783
Cheers, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
which curvature values. Can you send the output?
On Fri, 26 May 2006, Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
pretty much, although if you have saddle points the mean curvature can disappear (since one direction has positive and the other negative curvature) On Sat, 27 May 2006, Fornito, Alexander wrote:
No, I don't need signed values necessarily. So just to double-check then, higher mean curvature for averaged across a gyral ROI label would mean the gyrus has a more steeply peaked appearance, whereas high values for a sulcal label would, conversely, mean the sulcus resembles a shraply bended valley?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 10:21 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
p.s. sorry, the mean and Gaussian curvatures displayed in mris_anatomical_stats are absolute value. I forgot this, sorry. The integrate Gaussian curvature is actually a topological invariant, so doesn't tell you much about the surface. Do you really need signed mean curvaature averaged over a region? If so, you could specify -T curv, so that the "thickness" is actually the curvature, and it will give you the mean and std.
Bruce
On Fri, 26 May 2006, Fornito, Alexander wrote:
Yup. That looks fine.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 9:44 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
when you overlay the ?h.curv file on the inflated surface does it look correct? Are there both red and green regions? On Fri, 26 May 2006, Fornito, Alexander wrote:
I mainly interested in the mean curvature.
This is output for a gyral ROI:
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 395 1297 3.145 0.780 0.151 0.027 4.123 0.572
This is for a sulcal ROI;
% 1001365: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 647773 563 1693 2.992 0.567 0.121 0.068 48.616 4.783
Cheers, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 5/26/2006 8:32 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ROI Curvature
which curvature values. Can you send the output?
On Fri, 26 May 2006, Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 5/25/2006 9:09 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive. You can overlay the ?h.curv map to check.
cheers, Bruce On Thu, 25 May 2006, Fornito, Alexander wrote:
Hi, I have some labels that I've drawn, which correspond to the gyral crown and sulcal fundus of a given ROI. From what I understand, mean curvature provides an index of the convexity/concavity of the region. I would therefore have expected high positive values in the gyral ROI to represent a steeper peak in the curvature of the crown, with values closed to zero representing a more flattened gyrus. Converseley, I would have thought low negative values for the fundus ROI would represent a steeper peak in the opposite direction, with values closer to zero again reflecting flattened curvature. In reality, the values I get for both sulcal and gyral labels (using mris_anatomical_stats) tend to be both positive. Hoping someone could tell me what I'm missing?
Thanks in advance, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On Thursday 25 May 2006 17:44, Fornito, Alexander wrote:
Sorry, got it wrong way around. Either way, when I run mris_anatomical_stats on labels that I have created, I tend to get positive values for mean curvature for labels of both gyral crowns or sulcal fundi. Are the curvature values provided by mris_anatomical_stats unsigned?
'mris_curvature_stats' provides signed statistics on Gaussian and Mean curvatures. By default it does not calculate the principle curvatures, so it has to be explicitly told:
$>mris_curvature_stats -m -h 11 -G -F smoothwm <SUBJ> <hemi> <curvFile>
where
-m Show the min and max values of each curvature calculation
-h 11 Show a histogram of curvatures sorted into 11 bins
-G Calculate Gaussian statistics
-F smoothwm Use the 'smoothwm' surface for Gaussian statistics (otherwise default to the 'orig' surface which is probably what you don't want).
<SUBJ> The subject to process
<hemi> Hemisphere to process
<curvFile> Curvature file to process (does not affect the Gaussian / mean stats).
Cheers -=R
freesurfer@nmr.mgh.harvard.edu
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