Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in the first figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
Hi Rhuang,
On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm).
It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in the first
figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jenni
Thanks a lot for your reply.
Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Could you please tell me whether my understanding is correct or not?
Best wishes
Rhuang
On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote:
Hi Rhuang,
On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm).
It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in the first
figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you are refering to with the following descriptions:
the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni
Thanks a lot for your reply.
Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Could you please tell me whether my understanding is correct or not?
Best wishes
Rhuang
On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote:
Hi Rhuang,
On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm).
It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in the first
figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
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
Hi Jenni,
Many thanks for message.
I tried to go through the Freesurfer Tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial)
There are three sessions in Day-2, including Session_1a and Session_1b.
In Session_1a (FreeSurfer Tutorial: Group Analysis), the FSGD file was presented as a table. Several columns corresponds to # A B C # subject Age Gender ....
Session_1b follows Session_1a.
In Session_1b (just below the first figure), the sentence ' Next, load FSGD file lh.gender_age.glmdir/y.fsgd in the same directory by selecting File -> Load Group Descriptor File. ' implies the blue/red areas relating to the two groups (M, F), I think.
I would like to know which group (gender: M, F) has got thin thickness at the blue/red area in the first figure?
Any further suggestions please?
Rhuang
On Wednesday 09 May 2007 19:16, Jenni Pacheco wrote:
Hi,
I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you
are refering to with the following descriptions:
the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni
Thanks a lot for your reply.
Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Could you please tell me whether my understanding is correct or not?
Best wishes
Rhuang
On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote:
Hi Rhuang,
On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm).
It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in the first
figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
So the contrast used to perform this statistical test kept the two groups (male and female) constant and only looked for an interaction between thickness and age. So in this case the blue is where thickness and age are negatively correlated (as the age goes up the cortex gets thinner) and the red regions show areas where thickness and age are positively correlated (as the age goes up the cortex gets thicker). This is based on the contrast used to create the sig.mgh, shown in session 1a under day 2.
Does this help? Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni,
Many thanks for message.
I tried to go through the Freesurfer Tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial)
There are three sessions in Day-2, including Session_1a and Session_1b.
In Session_1a (FreeSurfer Tutorial: Group Analysis), the FSGD file was presented as a table. Several columns corresponds to # A B C # subject Age Gender ....
Session_1b follows Session_1a.
In Session_1b (just below the first figure), the sentence ' Next, load FSGD file lh.gender_age.glmdir/y.fsgd in the same directory by selecting File -> Load Group Descriptor File. ' implies the blue/red areas relating to the two groups (M, F), I think.
I would like to know which group (gender: M, F) has got thin thickness at the blue/red area in the first figure?
Any further suggestions please?
Rhuang
On Wednesday 09 May 2007 19:16, Jenni Pacheco wrote:
Hi,
I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you
are refering to with the following descriptions:
the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni
Thanks a lot for your reply.
Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Could you please tell me whether my understanding is correct or not?
Best wishes
Rhuang
On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote:
Hi Rhuang,
On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm).
It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in the first
figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
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
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
Hi, Jenni Hi, Nick
Many thanks for your explanations.
I agree with you that the inflated surface figure, the first figure of FsTutorial/Visualization, (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) constains information of the two groups' thickness
But the descriptions in Session_1a (FreeSurfer Tutorial: Group Analysis) show that the FSGD file is # A B C # subject Age Gender ... and the contrast vector can be selected (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/CreateContrastVectors) (1) [1 -1 0] for DOSS 'If you wanted to compare the thickness differences between Males and Females, while regressing out age you could use a contrast vector [1 -1 0]'. (2) [0 0 1] for DOSS 'If you wanted to make a direct comparison between thickness and age, regardless of gender, you could use the contrast vector [0 0 1]'
I would like to know the thickness differences between Males and Females.
If the contrast vector is [1 -1 0], does the blue/red area in the first figure of FsTutorial/Visualization show the interaction between the thickness and the two gender groups (M, F)? Which group has got thinner thickness at the red/blue area? Maybe the red/blue area relate to the intercept of average thickness of Male/Female at that area?
I really appreciate your further explanation.
Rhuang
On Wednesday 09 May 2007 20:48, you wrote:
Hi,
So the contrast used to perform this statistical test kept the two groups (male and female) constant and only looked for an interaction between thickness and age. So in this case the blue is where thickness and age are negatively correlated (as the age goes up the cortex gets thinner) and the red regions show areas where thickness and age are positively correlated (as the age goes up the cortex gets thicker). This is based on the contrast used to create the sig.mgh, shown in session 1a under day 2.
Does this help? Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni,
Many thanks for message.
I tried to go through the Freesurfer Tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial)
There are three sessions in Day-2, including Session_1a and Session_1b.
In Session_1a (FreeSurfer Tutorial: Group Analysis), the FSGD file was presented as a table. Several columns corresponds to # A B C # subject Age Gender ....
Session_1b follows Session_1a.
In Session_1b (just below the first figure), the sentence ' Next, load FSGD file lh.gender_age.glmdir/y.fsgd in the same directory by selecting File -> Load Group Descriptor File. ' implies the blue/red areas relating to the two groups (M, F), I think.
I would like to know which group (gender: M, F) has got thin thickness at the blue/red area in the first figure?
Any further suggestions please?
Rhuang
On Wednesday 09 May 2007 19:16, Jenni Pacheco wrote:
Hi,
I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you
are refering to with the following descriptions:
the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni
Thanks a lot for your reply.
Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Could you please tell me whether my understanding is correct or not?
Best wishes
Rhuang
On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote:
Hi Rhuang,
On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm).
It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in the first
figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
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
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
Ruiwang,
The first figure on the FsTutorial/Visualization page was made using a contrast of: (2) [0 0 1] for DOSS 'If you wanted to make a direct comparison between thickness and age, regardless of gender, you could use the contrast vector [0 0 1]' Therefore, the regions of red and blue are showing results for the direct comparison of thickness and age regardless of gender.
There is no figure showing the interaction between thickness and the two groups - we did not run that in this tutorial.
If you have your own copy of the tutorial data you could certainly run this comparison, but as it is there is no figure on the wiki that shows this because that contrast was not run. The only figures are showing the interaction between thickness and age regardless of gender.
Jenni -----Original Message----- From: Ruiwang Huang [mailto:r.huang@fz-juelich.de] Sent: Thursday, May 10, 2007 5:30 AM To: Freesurfer Mailing List Cc: Jenni Pacheco; Nick Schmansky Subject: Re: [Freesurfer] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?
Hi, Jenni Hi, Nick
Many thanks for your explanations.
I agree with you that the inflated surface figure, the first figure of FsTutorial/Visualization, (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) constains information of the two groups' thickness
But the descriptions in Session_1a (FreeSurfer Tutorial: Group Analysis) show that the FSGD file is # A B C # subject Age Gender ... and the contrast vector can be selected (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/CreateContrastVectors) (1) [1 -1 0] for DOSS 'If you wanted to compare the thickness differences between Males and Females, while regressing out age you could use a contrast vector [1 -1 0]'. (2) [0 0 1] for DOSS 'If you wanted to make a direct comparison between thickness and age, regardless of gender, you could use the contrast vector [0 0 1]'
I would like to know the thickness differences between Males and Females.
If the contrast vector is [1 -1 0], does the blue/red area in the first figure of FsTutorial/Visualization show the interaction between the thickness and the two gender groups (M, F)?
Which group has got thinner thickness at the red/blue area? Maybe the red/blue area relate to the intercept of average thickness of Male/Female at that area?
I really appreciate your further explanation.
Rhuang
On Wednesday 09 May 2007 20:48, you wrote:
Hi,
So the contrast used to perform this statistical test kept the two groups (male and female) constant and only looked for an interaction between thickness and age. So in this case the blue is where thickness and age are negatively correlated (as the age goes up the cortex gets thinner) and the red regions show areas where thickness and age are positively correlated (as the age goes up the cortex gets thicker). This is based on the contrast used to create the sig.mgh, shown in session 1a under day 2.
Does this help? Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni,
Many thanks for message.
I tried to go through the Freesurfer Tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial)
There are three sessions in Day-2, including Session_1a and Session_1b.
In Session_1a (FreeSurfer Tutorial: Group Analysis), the FSGD file was presented as a table. Several columns corresponds to # A B C # subject Age Gender ....
Session_1b follows Session_1a.
In Session_1b (just below the first figure), the sentence ' Next, load FSGD file lh.gender_age.glmdir/y.fsgd in the same directory by selecting File -> Load Group Descriptor File. ' implies the blue/red areas relating to the two groups (M, F), I think.
I would like to know which group (gender: M, F) has got thin thickness at the blue/red area in the first figure?
Any further suggestions please?
Rhuang
On Wednesday 09 May 2007 19:16, Jenni Pacheco wrote:
Hi,
I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you
are refering to with the following descriptions:
the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni
Thanks a lot for your reply.
Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Could you please tell me whether my understanding is correct or not?
Best wishes
Rhuang
On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote:
Hi Rhuang,
On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if
you
were displaying a cortical thickness map for an individual subject
the
color bar would then be showing the cortical thickness values (in
mm).
It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than
younger
subjects and the red regions show areas where younger subjects are significantly thinner than older subjects.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in
the
first
figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or
[-log10(p)]?
Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
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
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
Hi Jenni
Great. Really thanks.
Rhuang
On Thursday 10 May 2007 13:45, you wrote:
Ruiwang,
The first figure on the FsTutorial/Visualization page was made using a contrast of: (2) [0 0 1] for DOSS 'If you wanted to make a direct comparison between thickness and age, regardless of gender, you could use the contrast vector [0 0 1]' Therefore, the regions of red and blue are showing results for the direct comparison of thickness and age regardless of gender.
There is no figure showing the interaction between thickness and the two groups - we did not run that in this tutorial.
If you have your own copy of the tutorial data you could certainly run this comparison, but as it is there is no figure on the wiki that shows this because that contrast was not run. The only figures are showing the interaction between thickness and age regardless of gender.
Jenni -----Original Message----- From: Ruiwang Huang [mailto:r.huang@fz-juelich.de] Sent: Thursday, May 10, 2007 5:30 AM To: Freesurfer Mailing List Cc: Jenni Pacheco; Nick Schmansky Subject: Re: [Freesurfer] Does 'color scale bar' show the cortical thicknessor[-log10(p)]?
Hi, Jenni Hi, Nick
Many thanks for your explanations.
I agree with you that the inflated surface figure, the first figure of FsTutorial/Visualization, (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) constains information of the two groups' thickness
But the descriptions in Session_1a (FreeSurfer Tutorial: Group Analysis) show that the FSGD file is # A B C # subject Age Gender ... and the contrast vector can be selected (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/CreateContrastVectors ) (1) [1 -1 0] for DOSS 'If you wanted to compare the thickness differences between Males and Females, while regressing out age you could use a contrast vector [1 -1 0]'. (2) [0 0 1] for DOSS 'If you wanted to make a direct comparison between thickness and age, regardless of gender, you could use the contrast vector [0 0 1]'
I would like to know the thickness differences between Males and Females.
If the contrast vector is [1 -1 0], does the blue/red area in the first figure of FsTutorial/Visualization show the interaction between the thickness and the two gender groups (M, F)?
Which group has got thinner thickness at the red/blue area? Maybe the red/blue area relate to the intercept of average thickness of Male/Female at that area?
I really appreciate your further explanation.
Rhuang
On Wednesday 09 May 2007 20:48, you wrote:
Hi,
So the contrast used to perform this statistical test kept the two groups (male and female) constant and only looked for an interaction between thickness and age. So in this case the blue is where thickness and age are negatively correlated (as the age goes up the cortex gets thinner) and the red regions show areas where thickness and age are positively correlated (as the age goes up the cortex gets thicker). This is based on the contrast used to create the sig.mgh, shown in session 1a under day 2.
Does this help? Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni,
Many thanks for message.
I tried to go through the Freesurfer Tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial)
There are three sessions in Day-2, including Session_1a and Session_1b.
In Session_1a (FreeSurfer Tutorial: Group Analysis), the FSGD file was presented as a table. Several columns corresponds to # A B C # subject Age Gender ....
Session_1b follows Session_1a.
In Session_1b (just below the first figure), the sentence ' Next, load FSGD file lh.gender_age.glmdir/y.fsgd in the same directory by selecting File -> Load Group Descriptor File. ' implies the blue/red areas relating to the two groups (M, F), I think.
I would like to know which group (gender: M, F) has got thin thickness at the blue/red area in the first figure?
Any further suggestions please?
Rhuang
On Wednesday 09 May 2007 19:16, Jenni Pacheco wrote:
Hi,
I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you
are refering to with the following descriptions:
the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni
Thanks a lot for your reply.
Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Could you please tell me whether my understanding is correct or not?
Best wishes
Rhuang
On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote:
Hi Rhuang,
On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if
you
were displaying a cortical thickness map for an individual subject
the
color bar would then be showing the cortical thickness values (in
mm).
It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than
younger
subjects and the red regions show areas where younger subjects are significantly thinner than older subjects.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in
the
first
figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or
[-log10(p)]?
Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
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Rhuang,
The inflated surface figure shows the -log10(p) significance map of thickness vs. age, for both groups (male and female). When you click on a vertex to bring-up a plot, it is showing you the actual thickness data (in mm) for that vertex for each of the subjects. This is intended to search for possible outliers in your group. The plot is able to distinguish between male and female (red and blue) because that information is available to the plotter (but again, the significance map shown on the inflated surface is for both groups, because of the contrast vector supplied to mri_glmfit).
Nick
On Wed, 2007-05-09 at 19:48 +0200, Ruiwang Huang wrote:
Hi Jenni,
Many thanks for message.
I tried to go through the Freesurfer Tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial)
There are three sessions in Day-2, including Session_1a and Session_1b.
In Session_1a (FreeSurfer Tutorial: Group Analysis), the FSGD file was presented as a table. Several columns corresponds to # A B C # subject Age Gender ....
Session_1b follows Session_1a.
In Session_1b (just below the first figure), the sentence ' Next, load FSGD file lh.gender_age.glmdir/y.fsgd in the same directory by selecting File -> Load Group Descriptor File. ' implies the blue/red areas relating to the two groups (M, F), I think.
I would like to know which group (gender: M, F) has got thin thickness at the blue/red area in the first figure?
Any further suggestions please?
Rhuang
On Wednesday 09 May 2007 19:16, Jenni Pacheco wrote:
Hi,
I'm not sure where you are getting the descriptions below. This statistical map on the surface is actually looking at the correlations of thickness and age, not gender. Can you be more specific as to what you
are refering to with the following descriptions:
the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Jenni
On Wed, 9 May 2007, Ruiwang Huang wrote:
Hi Jenni
Thanks a lot for your reply.
Following the descriptions on FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) the 'color scale bar' indicates area coded in blue == cortical thickness of Female < that of Male (eg. 1mm <2mm), area coded in red == cortical thickness of Female < that of Male (eg. 3mm of Female >2mm of Male).
Could you please tell me whether my understanding is correct or not?
Best wishes
Rhuang
On Wednesday 09 May 2007 13:38, Jenni Pacheco wrote:
Hi Rhuang,
On that particular page the color bar is showing the sigificance (-log10(p)) for the group difference in that example. However, if you were displaying a cortical thickness map for an individual subject the color bar would then be showing the cortical thickness values (in mm).
It is showing the negative values to indicate the direction of the effect. Because of the way this analysis was set up the blue regions show areas where older subjects are significantly thinner than younger subjects and the red regions show areas where younger subjects are significantly thinner than older subjects.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruiwang Huang Sent: Wednesday, May 09, 2007 4:20 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Does 'color scale bar' show the cortical thickness or[-log10(p)]?
Dear All,
I am puzzled by the meaning of 'color scale bar', which appears in the first
figure of the FsTutorial/Visualization (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization)
Could you please let me know the meaning of colorbar? Does the 'color scale bar' show the cortical thickness or [-log10(p)]? Why the colorbar indicates the positive and negative value in the first figure?
Many thanks in advance
Rhuang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ruiwang Huang