Dear Freesurfer experts,
I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what about the surface area? Calculation based on pial or white matter? Or average the area of both of them.
Is the area of each vertex obtained by the average the area of triangles surrounding the vertex? In addition, where can I find the definition of meancurv, gauscurv, foldind, curvind? I do not find it in the fswiki.
Best, Feng
Hi Feng
we compute the surface area of each surface and store it separately. The ?h.area files are for the white surface and the ?h.area.pial for the pial
cheers Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote:
Dear Freesurfer experts, I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what about the surface area? Calculation based on pial or white matter? Or average the area of both of them. Is the area of each vertex obtained by the average the area of triangles surrounding the vertex? In addition, where can I find the definition of meancurv, gauscurv, foldind, curvind? I do not find it in the fswiki. Best, Feng
Thanks, Bruce
So, in the stats folder of each subject, the lh.aparc.a2009s.stats file provides surfarea of each region. This value is the area for the white surface, right?
Is the area of each vertex obtained by the average the area of triangles surrounding the vertex?
Best, Feng
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2015-10-06 20:25 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送：
Hi Feng
we compute the surface area of each surface and store it separately. The ?h.area files are for the white surface and the ?h.area.pial for the pial
cheers Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote:
Dear Freesurfer experts,
I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what about the surface area? Calculation based on pial or white matter? Or average the area of both of them.
Is the area of each vertex obtained by the average the area of triangles surrounding the vertex? In addition, where can I find the definition of meancurv, gauscurv, foldind, curvind? I do not find it in the fswiki.
Best, Feng
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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.
yes, that is correct Bruce
On Tue, 6 Oct 2015, chenhf_uestc wrote:
Thanks, Bruce So, in the stats folder of each subject, the lh.aparc.a2009s.stats file provides surfarea of each region. This value is the area for the white surface, right? Is the area of each vertex obtained by the average the area of triangles su rrounding the vertex? Best, Feng
发件人：Bruce Fischl <fischl@nmr.mgh.harvard.edu>发送时间：2015-10-06 20:25 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送： Hi Feng we compute the surface area of each surface and store it separately. The ?h.area files are for the white surface and the ?h.area.pial for the pial cheers Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote:
Dear Freesurfer experts, I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what ab
out
the surface area? Calculation based on pial or white matter? Or average t
he
area of both of them. Is the area of each vertex obtained by the average the area of triangles
?? ?> surrounding the vertex?
In addition, where can I find the definition of meancurv, gauscurv, foldi
nd,
curvind? I do not find it in the fswiki. Best, Feng
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0 The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
Thanks a lot, Bruce
If I want to compare the surface area between the patients and healthy control groups, which area file should I use? The area or the area.pial? Or I should compare both of them? If I should use both, is there any possibility that I would obtain different results from area and area.pial? I mean, in this case, a brain region has significantly different area but same (not significant) area.pial. How can I explain them in my research paper?
BTW, just out of curiosity, in the stats file such as lh.aparc.stats, why just thickness has the mean and std value, but other measures do not have the std value? SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd
Best, Feng
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2015-10-06 20:45 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送：
yes, that is correct Bruce
On Tue, 6 Oct 2015, chenhf_uestc wrote:
Thanks, Bruce So, in the stats folder of each subject, the lh.aparc.a2009s.stats file provides surfarea of each region. This value is the area for the white surface, right? Is the area of each vertex obtained by the average the area of triangles su rrounding the vertex? Best, Feng
发件人：Bruce Fischl <fischl@nmr.mgh.harvard.edu>发送时间：2015-10-06 20:25 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送：
Hi Feng
we compute the surface area of each surface and store it separately. The ?h.area files are for the white surface and the ?h.area.pial for the pial
cheers Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote:
Dear Freesurfer experts,
I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what ab
out
the surface area? Calculation based on pial or white matter? Or average t
he
area of both of them.
Is the area of each vertex obtained by the average the area of triangles
?? ?> surrounding the vertex?
In addition, where can I find the definition of meancurv, gauscurv, foldi
nd,
curvind? I do not find it in the fswiki.
Best, Feng
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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
_______________________________________________ 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 Feng
they are slightly different measures so which one you use really depends on your biological hypothesis.
For thickness there are multiple measures within each ROI but only one area (that of the whole ROI), so mean and std doesn't make sense.
cheers Bruce
On Wed, 7 Oct 2015, chenhf_uestc wrote:
Thanks a lot, Bruce If I want to compare the surface area between the patients and healthy control groups, which area file should I use? The area or the area.pial? Or I should compare both of them? If I should use both, is there any possibility that I would obtain different results from area and area.pial? I mean, in this case, a brain region has significantly different area but same (not significant) area.pial. How can I explain them in my research paper? BTW, just out of curiosity, in the stats file such as lh.aparc.stats, why just thickness has the mean and std value, but other measures do not have the std value? SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd Best, Feng
发件人：Bruce Fischl <fischl@nmr.mgh.harvard.edu>发送时间：2015-10-06 20:45 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送： yes, that is correct Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote:
Thanks, Bruce So, in the stats folder of each subject, the lh.aparc.a2009s.stats file provides surfarea of each region. This value
?? ?> is the area for the white surface, right?
Is the area of each vertex obtained by the average the area of triangles
?? ?su
rrounding the vertex? Best, Feng _________________________________________________________________________
___
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2015-10-06 20:25 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送： Hi Feng we compute the surface area of each surface and store it separately. The
?? ?
?h.area files are for the white surface and the ?h.area.pial for the pial
cheers Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote: > Dear Freesurfer experts, > > I have a question about the calculation of surface area. The cortical
?? ?> > thickness is the distance between the pial and white matter. But, what ?? ?ab
out > the surface area? Calculation based on pial or white matter? Or average
t
he > area of both of them. > > Is the area of each vertex obtained by the average the area of triangle
s ?? ?> surrounding the vertex?
> In addition, where can I find the definition of meancurv, gauscurv, fol
di
nd, > curvind? I do not find it in the fswiki. > > Best, > Feng > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0%C2%A0 The information in this e-mail is intended only for the person to whom it
i
s addressed. If you believe this e-mail was sent to you in error and the e-
ma
il contains patient information, please contact the Partners Compliance Help
Li
ne at http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
e
rror but does not contain patient information, please contact the sender and p
ro
perly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0 The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
I thought that we calculate the Surface area, MeanCurv, GausCurv, FoldInd and CurvInd in each vertex, and thus we can obtain the whole map on the surface. Subsequently, using the predefined atlas, we can further obtain the mean and std value in each brain region (because each vertex has a value). It looks like you do not calculate surface area and other measures in the aforementioned way, right?
From your words, it may be that the surface area is the summation of each vertex's area in each region, right? In contrast, for thickness, you compute the mean thickness across all the vertics. And of coz, I can compute the total thickness in each region like the area (summation of each vertex's thickness in each region), right?
Best, Feng
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2015-10-07 22:32 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送：
Hi Feng
they are slightly different measures so which one you use really depends on your biological hypothesis.
For thickness there are multiple measures within each ROI but only one area (that of the whole ROI), so mean and std doesn't make sense.
cheers Bruce
On Wed, 7 Oct 2015, chenhf_uestc wrote:
Thanks a lot, Bruce
If I want to compare the surface area between the patients and healthy control groups, which area file should I use? The area or the area.pial? Or I should compare both of them? If I should use both, is there any possibility that I would obtain different results from area and area.pial? I mean, in this case, a brain region has significantly different area but same (not significant) area.pial. How can I explain them in my research paper?
BTW, just out of curiosity, in the stats file such as lh.aparc.stats, why just thickness has the mean and std value, but other measures do not have the std value? SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd
Best, Feng
发件人：Bruce Fischl <fischl@nmr.mgh.harvard.edu>发送时间：2015-10-06 20:45 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送：
yes, that is correct Bruce
On Tue, 6 Oct 2015, chenhf_uestc wrote:
Thanks, Bruce So, in the stats folder of each subject, the lh.aparc.a2009s.stats file provides surfarea of each region. This value
?? ?> is the area for the white surface, right?
Is the area of each vertex obtained by the average the area of triangles
?? ?su
rrounding the vertex? Best, Feng
发件人：Bruce Fischl <fischl@nmr.mgh.harvard.edu>发送时间：2015-10-06 20:25 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送：
Hi Feng
we compute the surface area of each surface and store it separately. The
?? ?
?h.area files are for the white surface and the ?h.area.pial for the pial
cheers Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote:
Dear Freesurfer experts,
I have a question about the calculation of surface area. The cortical
?? ?> > thickness is the distance between the pial and white matter. But, what ?? ?ab
out
the surface area? Calculation based on pial or white matter? Or average
t
he
area of both of them.
Is the area of each vertex obtained by the average the area of triangle
s ?? ?> surrounding the vertex?
In addition, where can I find the definition of meancurv, gauscurv, fol
di
nd,
curvind? I do not find it in the fswiki.
Best, Feng
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
i
s addressed. If you believe this e-mail was sent to you in error and the e-
ma
il contains patient information, please contact the Partners Compliance Help
Li
ne at http://www.partners.org/complianceline . If the e-mail was sent to you in
e
rror but does not contain patient information, please contact the sender and p
ro
perly dispose of the e-mail.
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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
_______________________________________________ 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 Feng
thickness has a biological meaning as a point measure, but area does not. The area of any given triangle doesn't carry any biologically relevant information that I can think of, which is why we don't quantify the statistics of the area of individual triangles
cheers Bruce
On Wed, 7 Oct 2015, chenhf_uestc wrote:
I thought that we calculate the Surface area, MeanCurv, GausCurv, FoldInd and CurvInd in each vertex, and thus we can obtain the whole map on the surface. Subsequently, using the predefined atlas, we can further obtain the mean and std value in each brain region (because each vertex has a value). It looks like you do not calculate surface area and other measures in the aforementioned way, right? From your words, it may be that the surface area is the summation of each vertex's area in each region, right? In contrast, for thickness, you compute the mean thickness across all the vertics. And of coz, I can compute the total thickness in each region like the area (summation of each vertex's thickness in each region), right? Best, Feng
发件人：Bruce Fischl <fischl@nmr.mgh.harvard.edu>发送时间：2015-10-07 22:32 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送： Hi Feng they are slightly different measures so which one you use really depends on your biological hypothesis. For thickness there are multiple measures within each ROI but only one area (that of the whole ROI), so mean and std doesn't make sense. cheers Bruce On Wed, 7 Oct 2015, chenhf_uestc wrote:
Thanks a lot, Bruce If I want to compare the surface area between the patients and healthy control groups, which area file should I use? The area or the area.pial?
?? ?Or
I should compare both of them? If I should use both, is there any possibility that I would obtain different results from area and area.pial
? I
mean, in this case, a brain region has significantly different area but s
ame
(not significant) area.pial. How can I explain them in my research paper?
BTW, just out of curiosity, in the stats file such as lh.aparc.stats, why
just thickness has the mean and std value, but other measures do not have
the std value? SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd Best, Feng _________________________________________________________________________
___
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2015-10-06 20:45 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu 抄送： yes, that is correct Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote: > Thanks, Bruce So, in the stats folder of each subject, the > lh.aparc.a2009s.stats file provides surfarea of each region. This value
?? ?> is the area for the white surface, right?
> Is the area of each vertex obtained by the average the area of triangle
s ?? ?su
> rrounding the vertex? Best, Feng > > _______________________________________________________________________
__
___ > 发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu > 发送时间：2015-10-06 20:25 > 主题：Re: [Freesurfer] Query about the calculation of surface area > 收件人："Freesurfer support list"freesurfer@nmr.mgh.harvard.edu > 抄送： > > Hi Feng > > we compute the surface area of each surface and store it separately. Th
e ?? ?
> ?h.area files are for the white surface and the ?h.area.pial for the pi
al
> > cheers > Bruce > On > Tue, 6 Oct 2015, chenhf_uestc wrote: > > > Dear Freesurfer experts, > > > > I have a question about the calculation of surface area. The cortical
?? ?> > thickness is the distance between the pial and white matter. But, w hat ?? ?ab
> out > > the surface area? Calculation based on pial or white matter? Or avera
ge
t > he > > area of both of them. > > > > Is the area of each vertex obtained by the average the area of triang
le
s ?? ?> surrounding the vertex? > > In addition, where can I find the definition of meancurv, gauscurv, f
ol
di > nd, > > curvind? I do not find it in the fswiki. > > > > Best, > > Feng > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0%C2%A0%C2%... > > > The information in this e-mail is intended only for the person to whom
?? ?it
i > s > addressed. If you believe this e-mail was sent to you in error and the
?? ?e-
ma > il > contains patient information, please contact the Partners Compliance He
lp
Li > ne at > http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
?? ?in
e > rror > but does not contain patient information, please contact the sender and
p
ro > perly > dispose of the e-mail. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0%C2%A0 The information in this e-mail is intended only for the person to whom it
i
s addressed. If you believe this e-mail was sent to you in error and the e-
ma
il contains patient information, please contact the Partners Compliance Help
Li
ne at http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
e
rror but does not contain patient information, please contact the sender and p
ro
perly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0 The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
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chenhf_uestc