Re: [Freesurfer] Query about the calculation of surface area
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 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" 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 > 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" > 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 > > 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" > > 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/ma
Re: [Freesurfer] Query about the calculation of surface area
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 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" 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 > 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" > 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 > > 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" > > 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
Re: [Freesurfer] Query about the calculation of surface area
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 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" 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 > 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" > 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.
Re: [Freesurfer] Query about the calculation of surface area
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 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" 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 > 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" > 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. ___ 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.
Re: [Freesurfer] Query about the calculation of surface area
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 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" 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.
Re: [Freesurfer] Query about the calculation of surface area
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 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" 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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Query about the calculation of surface area
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 ___ 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] Query about the calculation of surface area
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___ 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.
