**Calculation of component size “Intensity” in NBS**

*National Institute for Physiological Sciences, SOKENDAI*

Hi,

I’m using the NBS toolbox to analyze differences between the results of two task conditions, in which I have two representative connectivity matrices for each subject. Regarding calculating the component size “intensity”, why does the NBS add up the t-values of each component minus the threshold value? I referred to the calculation of the variable test_stat_mat in the file NBS.stats.m. I would like to know the difference between this method and the calculation method that adds up the t-values of each component as they are, without subtracting the threshold.

Thank you for your time. I look forward to hearing from you soon.

Best regards,

Makoto

Hi makoto,

I'm not sure if I fully understand your question, but I think that you are referring to the distinction between the cluster mass and cluster extent statistics. For cluster mass, we add the test statistic across connections that comprise the connected component and that yeilds the statistic for the connected component. The threshold can then be substracted from the statistic so that the statistic reflects how much of an effect we have above and beyond the threshold. But it is not essential to subtract the threshold. I hope that I have understood your question correctly.

Andrew

*Originally posted by Makoto HAGIHARA:*

Hi,

I’m using the NBS toolbox to analyze differences between the results of two task conditions, in which I have two representative connectivity matrices for each subject. Regarding calculating the component size “intensity”, why does the NBS add up the t-values of each component minus the threshold value? I referred to the calculation of the variable test_stat_mat in the file NBS.stats.m. I would like to know the difference between this method and the calculation method that adds up the t-values of each component as they are, without subtracting the threshold.

Thank you for your time. I look forward to hearing from you soon.

Best regards,

Makoto

*National Institute for Physiological Sciences, SOKENDAI*

Hi Andrew,

Thanks for your quick reply. However, I’m still a little unclear.

I understood from your reply that it is not essential to subtract the threshold from the t-value in the “Intensity” calculation. So why did they choose to subtract the threshold in the NBS calculation? Or is it more common to subtract a threshold? I want to clarify this point.

Excerpt from file “NBS.stats.m (NBS1.2)”

%Compute a test statistic matrix

test_stat_mat=zeros(N,N);

if ~isempty(STATS.test_stat)

%Precomputed

test_stat_mat(ind_upper)=STATS.test_stat(1,:)**-STATS.thresh**;

test_stat_mat=(test_stat_mat+test_stat_mat');

else

%Not precomputed

test_stat_mat(ind_upper)=test_stat(1,:)**-STATS.thresh**;

test_stat_mat=(test_stat_mat+test_stat_mat');

end

if Intensity

%Measure size as intensity

sz_links(i)=sum(sum(adj(nodes,nodes).*test_stat_mat(nodes,nodes)))/2;

else

...

Thank you, in advance, for your time,

Best regards,

Makoto

*Originally posted by Andrew Zalesky:*

Hi makoto,

I'm not sure if I fully understand your question, but I think that you are referring to the distinction between the cluster mass and cluster extent statistics. For cluster mass, we add the test statistic across connections that comprise the connected component and that yeilds the statistic for the connected component. The threshold can then be substracted from the statistic so that the statistic reflects how much of an effect we have above and beyond the threshold. But it is not essential to subtract the threshold. I hope that I have understood your question correctly.

Andrew

Originally posted by Makoto HAGIHARA:

Hi,

I’m using the NBS toolbox to analyze differences between the results of two task conditions, in which I have two representative connectivity matrices for each subject. Regarding calculating the component size “intensity”, why does the NBS add up the t-values of each component minus the threshold value? I referred to the calculation of the variable test_stat_mat in the file NBS.stats.m. I would like to know the difference between this method and the calculation method that adds up the t-values of each component as they are, without subtracting the threshold.

Thank you for your time. I look forward to hearing from you soon.

Best regards,

Makoto

Hi Makoto,

the subtraction is not essential. It is for convenience, in that any positive t-statistics after the subtraction are above threshold and everything else is below threshold. The result should be the same with or without subtraction.

I think that some of the early imaging work from the 90's and 00's subtracted the threshold as well, and that might have been my inspiration.

Andrew

*Originally posted by Makoto HAGIHARA:*

Hi Andrew,

Thanks for your quick reply. However, I’m still a little unclear.

I understood from your reply that it is not essential to subtract the threshold from the t-value in the “Intensity” calculation. So why did they choose to subtract the threshold in the NBS calculation? Or is it more common to subtract a threshold? I want to clarify this point.

Excerpt from file “NBS.stats.m (NBS1.2)”

%Compute a test statistic matrix

test_stat_mat=zeros(N,N);

if ~isempty(STATS.test_stat)

%Precomputed

test_stat_mat(ind_upper)=STATS.test_stat(1,:)

-STATS.thresh;

test_stat_mat=(test_stat_mat+test_stat_mat');

else

%Not precomputed

test_stat_mat(ind_upper)=test_stat(1,:)

-STATS.thresh;

test_stat_mat=(test_stat_mat+test_stat_mat');

end

if Intensity

%Measure size as intensity

sz_links(i)=sum(sum(adj(nodes,nodes).*test_stat_mat(nodes,nodes)))/2;

else

...

Thank you, in advance, for your time,

Best regards,

Makoto

Originally posted by Andrew Zalesky:

Hi makoto,

I'm not sure if I fully understand your question, but I think that you are referring to the distinction between the cluster mass and cluster extent statistics. For cluster mass, we add the test statistic across connections that comprise the connected component and that yeilds the statistic for the connected component. The threshold can then be substracted from the statistic so that the statistic reflects how much of an effect we have above and beyond the threshold. But it is not essential to subtract the threshold. I hope that I have understood your question correctly.

Andrew

Originally posted by Makoto HAGIHARA:

Hi,

Thank you for your time. I look forward to hearing from you soon.

Best regards,

Makoto

*National Institute for Physiological Sciences, SOKENDAI*

Hi,

Thank you again for your quick and helpful reply. My question has been resolved.

Best regards,

Makoto

*Originally posted by Andrew Zalesky:*

Hi Makoto,

the subtraction is not essential. It is for convenience, in that any positive t-statistics after the subtraction are above threshold and everything else is below threshold. The result should be the same with or without subtraction.

I think that some of the early imaging work from the 90's and 00's subtracted the threshold as well, and that might have been my inspiration.

Andrew

Originally posted by Makoto HAGIHARA:

Hi Andrew,

Thanks for your quick reply. However, I’m still a little unclear.

I understood from your reply that it is not essential to subtract the threshold from the t-value in the “Intensity” calculation. So why did they choose to subtract the threshold in the NBS calculation? Or is it more common to subtract a threshold? I want to clarify this point.

Excerpt from file “NBS.stats.m (NBS1.2)”

%Compute a test statistic matrix

test_stat_mat=zeros(N,N);

if ~isempty(STATS.test_stat)

%Precomputed

test_stat_mat(ind_upper)=STATS.test_stat(1,:)

-STATS.thresh;

test_stat_mat=(test_stat_mat+test_stat_mat');

else

%Not precomputed

test_stat_mat(ind_upper)=test_stat(1,:)

-STATS.thresh;

test_stat_mat=(test_stat_mat+test_stat_mat');

end

if Intensity

%Measure size as intensity

sz_links(i)=sum(sum(adj(nodes,nodes).*test_stat_mat(nodes,nodes)))/2;

else

...

Thank you, in advance, for your time,

Best regards,

Makoto

Originally posted by Andrew Zalesky:

Hi makoto,

Andrew

Originally posted by Makoto HAGIHARA:

Hi,

Thank you for your time. I look forward to hearing from you soon.

Best regards,

Makoto