correlation matrix

Submitted by iidaka on Tue, 02/04/2014 - 01:09

Dear all,

I am moving from DPARSF basic edition to advanced edition to compute intrinsic connectivity between the AAL ROIs. In the basic version there were files named subject01_AALTC.mat containing detrended, filtered, and covariates removed time course of 90 AAL ROIs.

My first question is that the same file in the advanced edition is now named ROISignals_subject01.mat?

Second, when chosing AAL template in the advanced version,  it uses 116 ROIs including cerebellum but not 90 ROIs as in the basic version ? Can I reduce the number of ROIs from 116 to 90?

Do ROICorrelation_subject01.mat and ROICorrelation_FisherZ_subject01.mat contain 116 x 116 correlation matrix of ROISignals_subject01.mat and its Z-transformed matrix?

Regards,

Tetsuya

Nagoya University, Graduate School of Medicine

 

Forums:

YAN Chao-Gan

Tue, 02/04/2014 - 02:01

Hi Tetsuya,

1. Yes, the time courses are stored in ROISignals_subject01.mat.

2. Simply choose first 1 - 90 columns, you can have the save 90 ROI setting as in the basic version.

3. Yes, that's correct. Those are the 116 x 116 correlation matrix and corresponded Fisher's r-to-z matrix. You can choose the submatrix of ROICorrelation(1:90,1:90) to get the 90 x 90 matrix.

Best,

Chao-Gan

iidaka

Tue, 02/04/2014 - 02:10






Hi,

 

Thank you for comments.

 

Tetsuya

 

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Sent: Tuesday, February 04, 2014 11:01 AM


Subject: Re: [RFMRI] correlation matrix

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

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Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Tetsuya,


1. Yes, the time courses are stored in ROISignals_subject01.mat.


2. Simply choose first 1 - 90 columns, you can have the save 90 ROI setting
as in the basic version.


3. Yes, that's correct. Those are the 116 x 116 correlation matrix and
corresponded Fisher's r-to-z matrix. You can choose the submatrix of
ROICorrelation(1:90,1:90) to get the 90 x 90 matrix.


Best,


Chao-Gan


Online version of this post: href="http://www.rfmri.org/comment/3023#comment-3023">http://www.rfmri.org/comment/3023#comment-3023



iidaka

Wed, 02/05/2014 - 02:00






Dear all,

 

I encountered an error message in FC analysis in DPARSF advanced
edition.

There was no ARWSDFCB volume in the last subject “Olin_50123”.

Other processes before this part look normal.

 

Your comment is very much appreciated.

 

Tetsuya

 

***************************

Read 3D EPI functional images:
"C:\DPARSF\Olin\FunImgARWSDFC\Olin_50124".

 

Read 3D EPI functional images:
"C:\DPARSF\Olin\FunImgARWSDFC\Olin_50123".

 

??? error ==> interp1 at 184

 

error ==> y_Scrubbing at 69

   AllVolume = interp1(x,AllVolume,xi,ScrubbingMethod);

*****************************

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

 



Sent: Tuesday, February 04, 2014 11:10 AM


Subject: Re: [RFMRI] correlation matrix

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

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Commented by Tetsuya Iidaka (iidaka)



Hi,

 

Thank you for comments.

 

Tetsuya

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

 



Sent: Tuesday, February 04, 2014 11:01 AM


Subject: Re: [RFMRI] correlation matrix

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

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Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Tetsuya,


1. Yes, the time courses are stored in ROISignals_subject01.mat.


2. Simply choose first 1 - 90 columns, you can have the save 90 ROI setting
as in the basic version.


3. Yes, that's correct. Those are the 116 x 116 correlation matrix and
corresponded Fisher's r-to-z matrix. You can choose the submatrix of
ROICorrelation(1:90,1:90) to get the 90 x 90 matrix.


Best,


Chao-Gan


Online version of this post: href="http://www.rfmri.org/comment/3023#comment-3023">http://www.rfmri.org/comment/3023#comment-3023




Online version of this post: href="http://www.rfmri.org/comment/3024#comment-3024">http://www.rfmri.org/comment/3024#comment-3024



YAN Chao-Gan

Thu, 02/06/2014 - 15:23

Hi Tetsuya,

The error happens in interpolation. I suspect that this subject (Olin_50123) may have very big head motion and all the time points may be scrubbed according to the FD threshold you set. You can check his/her FD numbers in RealignParameters/Olin_50123/FD***.txt.

Best,

Chao-Gan

iidaka

Fri, 02/07/2014 - 01:10






Hi, Chao-Gan

 

Thank you for response.

 

Certainly, FD values of this particular subject was larger than other
subjects.

To avoid this error, simply, is it neccesary to increase FD value for
scrubbing

or delete this subject from the dataset?

 

Regards,

 

tetsuya

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

 



Sent: Friday, February 07, 2014 12:23 AM


Subject: Re: [RFMRI] correlation matrix

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

[To post a comment, please reply to rfmri.org@gmail.com
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Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Tetsuya,


The error happens in interpolation. I suspect that this subject (Olin_50123)
may have very big head motion and all the time points may be scrubbed according
to the FD threshold you set. You can check his/her FD numbers in
RealignParameters/Olin_50123/FD***.txt.


Best,


Chao-Gan


Online version of this post: href="http://www.rfmri.org/comment/3026#comment-3026">http://www.rfmri.org/comment/3026#comment-3026



YAN Chao-Gan

Sun, 02/09/2014 - 21:35

Hi Tetsuya,

In such a case, I will suggest you to delete this subject if the head motion is extremely large. You can check how many time points left with your FD threshold. The results based on too few time points are not reliable.

Best,

Chao-Gan

iidaka

Fri, 02/14/2014 - 00:40






Dear all,

 

I was running DPARSF advanced edition to compute correlation matrix of AAL
template.

I found that number of regions in the ROISignals_subjects01.mat differed
between the

subjects. There were files that contained 116, 107, and 102 time courses.
Why is this?

 

tetsuya

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

 



Sent: Monday, February 10, 2014 6:35 AM


Subject: Re: [RFMRI] correlation matrix

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

[To post a comment, please reply to rfmri.org@gmail.com
ABOVE this line]

 

Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Tetsuya,


In such a case, I will suggest you to delete this subject if the head motion
is extremely large. You can check how many time points left with your FD
threshold. The results based on too few time points are not reliable.


Best,


Chao-Gan


Online version of this post: href="http://rfmri.org/comment/3029#comment-3029">http://rfmri.org/comment/3029#comment-3029



YAN Chao-Gan

Fri, 02/14/2014 - 19:53

Hi Tetsuya,

This is weird. Could you post your setting here (a snapshot of the GUI)?

Best,

Chao-Gan

iidaka

Mon, 02/17/2014 - 00:50






Thank you for response.

 

Actually, I re-ran the analysis and found that all ROISignal.mat files had

116 time courses.  I apologize for bothering you, probably, something
was

incorrect in data setting. But for confirmation, I attach GUI of my
DPARSF

setting.

 

Furthermore, in some of the subjects, time course had repetitions of the

same value as in the attached mat file. Is this the product of data
scrubing?

My setting was FD = 0.5 and nearest neighbour interpolation.

 

Regards,

 

Tetsuya

 

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

 



Sent: Saturday, February 15, 2014 4:53 AM


Subject: Re: [RFMRI] correlation matrix

 

style="FONT-SIZE: small; FONT-FAMILY: 'Calibri'; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; TEXT-DECORATION: none; DISPLAY: inline">

[To post a comment, please reply to rfmri.org@gmail.com
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Commented by YAN Chao-Gan (YAN Chao-Gan)

Hi Tetsuya,


This is weird. Could you post your setting here (a snapshot of the GUI)?


Best,


Chao-Gan


Online version of this post: href="http://rfmri.org/comment/3032#comment-3032">http://rfmri.org/comment/3032#comment-3032



YAN Chao-Gan

Mon, 02/17/2014 - 15:51

 

Hi Tetsuya,

Good to know that the number of time series are the same. BTW, Attachment can only via website instead of email.

For those subjects, all the time series are with the same values? What are the values? And how many time points left for them after scrubbing?

Best,

Chao-Gan

iidaka

Tue, 02/18/2014 - 01:30

Hi, image is uploaded.

tetsuya

This is the first column of ROISignal.mat

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YAN Chao-Gan

Tue, 02/18/2014 - 21:44

Hi,

Seems there were big head movements for this subject (through the NN interpolation). But all the columns should not have the exact same values (different voxels should have different values). Did you check the data, is there anything odd?

Best,

Chao-Gan

iidaka

Wed, 02/19/2014 - 04:08

Hi,

Not all columns are the same.

tetsuya

 

 0 0
0 0
0 0
0 0
0 0
0 0
-0.686671256552476 -0.132383132055067
-0.902382223255756 0.0673311685198944
-0.690875177251507 0.221868175307304
-0.782266318780029 0.223833756188349
-0.481744829168931 0.310882743785879
-0.481744829168931 0.310882743785879
-0.481744829168931 0.310882743785879
-0.481744829168931 0.310882743785879
-0.481744829168931 0.310882743785879
-0.481744829168931 0.310882743785879
-0.481744829168931 0.310882743785879