Re: [Freesurfer] Questions about the correction methods in Surfstat

[MCLAREN, Donald]

>The output figure is attached. In the colorbar of the figure, left
represents cluster corrected p value and right one represents the vertex
>corrected p value, right?
Right.

>So, the warm color region in the figure can be survived by the RFT vertex
correction, and the cool color region in the figure can be >survived by the
RFT cluster correction, right?
Right. RFT vertex correction is not a correct definition, it is a RFT
correction based on the maximum peak in contrast with the larger cluster
extent approach.

>If so, the regions with either warm or cool color region that can be
survived after correction. When I report the results, I can report the
>regions with warm color (vertex level correction) or report the regions
with cool color (cluster level correction), right?
Both thresholdings can be reported but I prefer peak thresholds (warm
colors) due to the lack of spatial specificity with clustering thresholds.

>In addtion, how can I understand the region overlapped by the warm and
cool color (like he postier cingulate cortex), can >simultaneously pass
double correction of vertex level and cluster level?
It is not a double corrections. The figure simply shows two different RFT
thresholding approaches.

The final question is about the RFT cluster correction method, in the SPM
or other software (like REST). Generally, on the cluster level correction,
you should be based on a voxel (vertex) uncorrected height threshold of
e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g.,
p<0.05, right? What is the detailed correction procedure in the Surfstat
software?
Exactly the same, p=0.001 for defining supra-threshold clusters and p=0.05
for RFT correction.

Regards, Felix.

Best Regards,
Donald McLaren, PhD


On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc  wrote:

> Dear Surfstat Users,
>
> I have a question about the RFT correction method in the Surfstat(
> http://www.math.mcgill.ca/keith/surfstat/).
> In the online manual, the command to perform RFT correction is as follows:
> [ pval, peak, clus ] = SurfStatP( slm, mask );
>
> pval.P contains P-values for peaks, and pval.C contains P-values for
> clusters. This special structure is recognised by SurfStatView which draws
> the figure in a special way:
>
> SurfStatView( pval, avsurf, 'Males-females removing age' );
>
> The output figure is attached. In the colorbar of the figure, left
> represents cluster corrected p value and right one represents the vertex
> corrected p value, right? So, the warm color region in the figure can be
> survived by the RFT vertex correction, and the cool color region in the
> figure can be survived by the RFT cluster correction, right? If so, the
> regions with either warm or cool color region that can be survived after
> correction. When I report the results, I can report the regions with warm
> color (vertex level correction) or report the regions with cool color
> (cluster level correction), right?
>
> In addtion, how can I understand the region overlapped by the warm and
> cool color (like he postier cingulate cortex), can simultaneously pass
> double correction of vertex level and cluster level?
>
> The final question is about the RFT cluster correction method, in the SPM
> or other software (like REST). Generally, on the cluster level correction,
> you should be based on a voxel (vertex) uncorrected height threshold of
> e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g.,
> p<0.05, right? What is the detailed correction procedure in the Surfstat
> software?
>
> Any help would be greatly appreciate.
>
> 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] Questions about the correction methods in Surfstat

[chenhf_uestc]

I see.
Thanks a lot, Donald

Best,
Feng



发件人："MCLAREN, Donald" <mclaren.don...@gmail.com>
发送时间：2015-10-07 11:01
主题：Re: [Freesurfer] Questions about the correction methods in Surfstat
收件人："Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
抄送：

>The output figure is attached. In the colorbar of the figure, left represents 
>cluster corrected p value and right one represents the vertex >corrected p 
>value, right? 

Right.


>So, the warm color region in the figure can be survived by the RFT vertex 
>correction, and the cool color region in the figure can be >survived by the 
>RFT cluster correction, right? 
Right. RFT vertex correction is not a correct definition, it is a RFT 
correction based on the maximum peak in contrast with the larger cluster extent 
approach.  

>If so, the regions with either warm or cool color region that can be survived 
>after correction. When I report the results, I can report the >regions with 
>warm color (vertex level correction) or report the regions with cool color 
>(cluster level correction), right?

Both thresholdings can be reported but I prefer peak thresholds (warm colors) 
due to the lack of spatial specificity with clustering thresholds.


>In addtion, how can I understand the region overlapped by the warm and cool 
>color (like he postier cingulate cortex), can >simultaneously pass double 
>correction of vertex level and cluster level?

It is not a double corrections. The figure simply shows two different RFT 
thresholding approaches.


The final question is about the RFT cluster correction method, in the SPM or 
other software (like REST). Generally, on the cluster level correction, you 
should be based on a voxel (vertex) uncorrected height threshold of e.g. 
p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, 
right? What is the detailed correction procedure in the Surfstat software?

Exactly the same, p=0.001 for defining supra-threshold clusters and p=0.05 for 
RFT correction.



Regards, Felix.


Best Regards, 
Donald McLaren, PhD




On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc <chenhf_ue...@163.com> wrote:

Dear Surfstat Users,

I have a question about the RFT correction method in the 
Surfstat(http://www.math.mcgill.ca/keith/surfstat/).
In the online manual, the command to perform RFT correction is as follows:
[ pval, peak, clus ] = SurfStatP( slm, mask ); 

pval.P contains P-values for peaks, and pval.C contains P-values for clusters. 
This special structure is recognised by SurfStatView which draws the figure in 
a special way:

SurfStatView( pval, avsurf, 'Males-females removing age' ); 

The output figure is attached. In the colorbar of the figure, left represents 
cluster corrected p value and right one represents the vertex corrected p 
value, right? So, the warm color region in the figure can be survived by the 
RFT vertex correction, and the cool color region in the figure can be survived 
by the RFT cluster correction, right? If so, the regions with either warm or 
cool color region that can be survived after correction. When I report the 
results, I can report the regions with warm color (vertex level correction) or 
report the regions with cool color (cluster level correction), right?

In addtion, how can I understand the region overlapped by the warm and cool 
color (like he postier cingulate cortex), can simultaneously pass double 
correction of vertex level and cluster level? 

The final question is about the RFT cluster correction method, in the SPM or 
other software (like REST). Generally, on the cluster level correction, you 
should be based on a voxel (vertex) uncorrected height threshold of e.g. 
p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, 
right? What is the detailed correction procedure in the Surfstat software?

Any help would be greatly appreciate.

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/compliancel

Re: [Freesurfer] Questions about the correction methods in Surfstat

[dgw]

Hi Feng,

This is not the surfstat list. You may want to check their webpage to
see how to get help and documentation.

hth
d

On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc  wrote:
> Dear Surfstat Users,
>
> I have a question about the RFT correction method in the
> Surfstat(http://www.math.mcgill.ca/keith/surfstat/).
> In the online manual, the command to perform RFT correction is as follows:
> [ pval, peak, clus ] = SurfStatP( slm, mask );
>
> pval.P contains P-values for peaks, and pval.C contains P-values for
> clusters. This special structure is recognised by SurfStatView which draws
> the figure in a special way:
>
> SurfStatView( pval, avsurf, 'Males-females removing age' );
>
> The output figure is attached. In the colorbar of the figure, left
> represents cluster corrected p value and right one represents the vertex
> corrected p value, right? So, the warm color region in the figure can be
> survived by the RFT vertex correction, and the cool color region in the
> figure can be survived by the RFT cluster correction, right? If so, the
> regions with either warm or cool color region that can be survived after
> correction. When I report the results, I can report the regions with warm
> color (vertex level correction) or report the regions with cool color
> (cluster level correction), right?
>
> In addtion, how can I understand the region overlapped by the warm and cool
> color (like he postier cingulate cortex), can simultaneously pass double
> correction of vertex level and cluster level?
>
> The final question is about the RFT cluster correction method, in the SPM or
> other software (like REST). Generally, on the cluster level correction, you
> should be based on a voxel (vertex) uncorrected height threshold of e.g.
> p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05,
> right? What is the detailed correction procedure in the Surfstat software?
>
> Any help would be greatly appreciate.
>
> 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

[Freesurfer] Questions about the correction methods in Surfstat

[chenhf_uestc]

Dear Surfstat Users,

I have a question about the RFT correction method in the 
Surfstat(http://www.math.mcgill.ca/keith/surfstat/).
In the online manual, the command to perform RFT correction is as follows:
[ pval, peak, clus ] = 
SurfStatP( slm, mask );


pval.P contains P-values for peaks, and pval.C contains P-values for clusters. 
This special structure is recognised by SurfStatView which draws the figure in 
a special way:

SurfStatView( pval, avsurf, 'Males-females removing age' ); 

The output figure is attached. In the colorbar of the figure, left represents 
cluster corrected p value and right one represents the vertex corrected p 
value, right? So, the warm color region in the figure can be survived by the 
RFT vertex correction, and the cool color region in the figure can be survived 
by the RFT cluster correction, right? If so, the regions with either warm or 
cool color region that can be survived after correction. When I report the 
results, I can report the regions with warm color (vertex level correction) or 
report the regions with cool color (cluster level correction), right?

In addtion, how can I understand the region overlapped by the warm and cool 
color (like he postier cingulate cortex), can simultaneously pass double 
correction of vertex level and cluster level? 

The final question is about the RFT cluster correction method, in the SPM or 
other software (like REST). Generally, on the cluster level correction, you 
should be based on a voxel (vertex) uncorrected height threshold of e.g. 
p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, 
right? What is the detailed correction procedure in the Surfstat software?

Any help would be greatly appreciate.

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.