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**ROC curve analysis**Showing 1-7 of 7 posts

Nov 26, 2017 06:11 AM | Hua Yu

ROC curve analysis

Dear experts,

Recently, I made a two sample t test to compare the global functional connectivity between patients' group and HC group, and I did find some group differences. Now I want to see if the group FC connectivity differences could clarify the two groups , and what I supposed to do was to extract the FC value to do some simple ROC curve analysis in SPSS. Do you have suggestion about this?

Looking forward for your reply,

Many thanks,

Hua

Recently, I made a two sample t test to compare the global functional connectivity between patients' group and HC group, and I did find some group differences. Now I want to see if the group FC connectivity differences could clarify the two groups , and what I supposed to do was to extract the FC value to do some simple ROC curve analysis in SPSS. Do you have suggestion about this?

Looking forward for your reply,

Many thanks,

Hua

Nov 26, 2017 02:11 PM | Andrew Zalesky

RE: ROC curve analysis

Hi Hua,

The NBS manual provides detailed instructions about how to extract FC values from significant subnetworks. It can be downloaded from NITRC.

Andrew

The NBS manual provides detailed instructions about how to extract FC values from significant subnetworks. It can be downloaded from NITRC.

Andrew

*Originally posted by Hua Yu:*Dear experts,

Recently, I made a two sample t test to compare the global functional connectivity between patients' group and HC group, and I did find some group differences. Now I want to see if the group FC connectivity differences could clarify the two groups , and what I supposed to do was to extract the FC value to do some simple ROC curve analysis in SPSS. Do you have suggestion about this?

Looking forward for your reply,

Many thanks,

Hua

Recently, I made a two sample t test to compare the global functional connectivity between patients' group and HC group, and I did find some group differences. Now I want to see if the group FC connectivity differences could clarify the two groups , and what I supposed to do was to extract the FC value to do some simple ROC curve analysis in SPSS. Do you have suggestion about this?

Looking forward for your reply,

Many thanks,

Hua

Nov 27, 2017 08:11 AM | Hua Yu

RE: ROC curve analysis

Dear Andrew,

Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua

Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua

Nov 27, 2017 03:11 PM | Andrew Zalesky

RE: ROC curve analysis

Hi Hua Yu,

for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16?

YES THIS IS CORRECT.

Andrew

for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16?

YES THIS IS CORRECT.

Andrew

*Originally posted by Hua Yu:*Dear Andrew,

Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua

Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua

Nov 29, 2017 05:11 AM | Hua Yu

RE: ROC curve analysis

Dear Andrew,

Sorry to bother you so much. I think there's something still wrong with the code. First, let me make a brief introduction of my analysis. I divided my patient's and HCs' brain according to Dosenbach's template in Dpabi which has 160 nodes and it generated 160x160 matrix for each subject. Now, I want to extract the connectivity coefficient for each pair of nodes that showed group connectivity difference which I uploaded before as you can see. However, every time when I type i=9, j=128 or i=14, j=144 or i=16, j=144 specifically for each pair of node number, I would meet with the same problem showing that "Index exceeds matrix dimensions."

Can you help me solve this problem or do you need me to provide more information about my analysis?

Sincerely,

Hua

Sorry to bother you so much. I think there's something still wrong with the code. First, let me make a brief introduction of my analysis. I divided my patient's and HCs' brain according to Dosenbach's template in Dpabi which has 160 nodes and it generated 160x160 matrix for each subject. Now, I want to extract the connectivity coefficient for each pair of nodes that showed group connectivity difference which I uploaded before as you can see. However, every time when I type i=9, j=128 or i=14, j=144 or i=16, j=144 specifically for each pair of node number, I would meet with the same problem showing that "Index exceeds matrix dimensions."

Can you help me solve this problem or do you need me to provide more information about my analysis?

Sincerely,

Hua

*Originally posted by Andrew Zalesky:*Hi Hua
Yu,

for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16?

YES THIS IS CORRECT.

Andrew

for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16?

YES THIS IS CORRECT.

Andrew

*Originally posted by Hua Yu:*Dear Andrew,

Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua

Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua

Nov 29, 2017 04:11 PM | Andrew Zalesky

RE: ROC curve analysis

Hi Hua,

I'm not sure what might be causing this issue. You might want to seek assistance from a colleague with Matlab expertise.

Andrew

I'm not sure what might be causing this issue. You might want to seek assistance from a colleague with Matlab expertise.

Andrew

*Originally posted by Hua Yu:*Dear
Andrew,

Sorry to bother you so much. I think there's something still wrong with the code. First, let me make a brief introduction of my analysis. I divided my patient's and HCs' brain according to Dosenbach's template in Dpabi which has 160 nodes and it generated 160x160 matrix for each subject. Now, I want to extract the connectivity coefficient for each pair of nodes that showed group connectivity difference which I uploaded before as you can see. However, every time when I type i=9, j=128 or i=14, j=144 or i=16, j=144 specifically for each pair of node number, I would meet with the same problem showing that "Index exceeds matrix dimensions."

Can you help me solve this problem or do you need me to provide more information about my analysis?

Sincerely,

Hua

Sorry to bother you so much. I think there's something still wrong with the code. First, let me make a brief introduction of my analysis. I divided my patient's and HCs' brain according to Dosenbach's template in Dpabi which has 160 nodes and it generated 160x160 matrix for each subject. Now, I want to extract the connectivity coefficient for each pair of nodes that showed group connectivity difference which I uploaded before as you can see. However, every time when I type i=9, j=128 or i=14, j=144 or i=16, j=144 specifically for each pair of node number, I would meet with the same problem showing that "Index exceeds matrix dimensions."

Can you help me solve this problem or do you need me to provide more information about my analysis?

Sincerely,

Hua

*Originally posted by Andrew Zalesky:*Hi Hua
Yu,

for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16?

YES THIS IS CORRECT.

Andrew

Dear Andrew,

Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua

for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16?

YES THIS IS CORRECT.

Andrew

*Originally posted by Hua Yu:*Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua

Dec 1, 2017 03:12 AM | Hua Yu

RE: ROC curve analysis

Dear Andrew,

Thank you so much. Finally, I solved my problems and the code in the manual is totally right!

Many thanks again. You are so helpful.

Hua

Thank you so much. Finally, I solved my problems and the code in the manual is totally right!

Many thanks again. You are so helpful.

Hua

*Originally posted by Andrew Zalesky:*Hi Hua,

I'm not sure what might be causing this issue. You might want to seek assistance from a colleague with Matlab expertise.

Andrew

I'm not sure what might be causing this issue. You might want to seek assistance from a colleague with Matlab expertise.

Andrew

*Originally posted by Hua Yu:*Dear
Andrew,

Sorry to bother you so much. I think there's something still wrong with the code. First, let me make a brief introduction of my analysis. I divided my patient's and HCs' brain according to Dosenbach's template in Dpabi which has 160 nodes and it generated 160x160 matrix for each subject. Now, I want to extract the connectivity coefficient for each pair of nodes that showed group connectivity difference which I uploaded before as you can see. However, every time when I type i=9, j=128 or i=14, j=144 or i=16, j=144 specifically for each pair of node number, I would meet with the same problem showing that "Index exceeds matrix dimensions."

Can you help me solve this problem or do you need me to provide more information about my analysis?

Sincerely,

Hua

Hi Hua
Yu,

for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16?

YES THIS IS CORRECT.

Andrew

Dear Andrew,

Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua

Sorry to bother you so much. I think there's something still wrong with the code. First, let me make a brief introduction of my analysis. I divided my patient's and HCs' brain according to Dosenbach's template in Dpabi which has 160 nodes and it generated 160x160 matrix for each subject. Now, I want to extract the connectivity coefficient for each pair of nodes that showed group connectivity difference which I uploaded before as you can see. However, every time when I type i=9, j=128 or i=14, j=144 or i=16, j=144 specifically for each pair of node number, I would meet with the same problem showing that "Index exceeds matrix dimensions."

Can you help me solve this problem or do you need me to provide more information about my analysis?

Sincerely,

Hua

*Originally posted by Andrew Zalesky:*for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16?

YES THIS IS CORRECT.

Andrew

*Originally posted by Hua Yu:*

Now I had the nbs.NBS con_mat file, and it stores the nodes information which showed significant group difference. The results comprised 1 significant network with 8 connctions. The binary connectivity val =

(12,16) 1

(4,32) 1

(9,46) 1

(12,46) 1

(32,46) 1

(9,128) 1

(16,144) 1

(19,144) 1

For the connectivity strength which I want to extract for each connection, how should I set the value of ' i & j', for example, if I want to extract the connectivity strength between node 12 and node 16, should I set the i=12, j=16? However, this seems not right.

i=1; %Specify node 1 here

j=2; %Specify node 2 here

global nbs; N=nbs.STATS.N; ind_upper=find(triu(ones(N,N),1)); cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper); cross_ref=cross_ref+cross_ref'; ind=cross_ref(i,j); fprintf('%0.2f\n',nbs.GLM.y(:,ind));

Can you help me modify the code or explain a little bit more about it?

Looking forward for you reply,

Sincerely,

Hua