correlation matrix

Submitted by iidaka on

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

 

YAN Chao-Gan

Tue, 02/04/2014 - 02:01

Permalink

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

Hi,
 
Thank you for comments.
 
Tetsuya
 
 
Sent: Tuesday, February 04, 2014 11:01 AM
Subject: Re: [RFMRI] correlation matrix
 
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]
 
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: http://www.rfmri.org/comment/3023#comment-3023


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);
*****************************
 
 
Sent: Tuesday, February 04, 2014 11:10 AM
Subject: Re: [RFMRI] correlation matrix
 
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]
 
Commented by Tetsuya Iidaka (iidaka)
Hi,
 
Thank you for comments.
 
Tetsuya
 
 
Sent: Tuesday, February 04, 2014 11:01 AM
Subject: Re: [RFMRI] correlation matrix
 
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]
 
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: http://www.rfmri.org/comment/3023#comment-3023



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


YAN Chao-Gan

Thu, 02/06/2014 - 15:23

Permalink

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

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
 
 
Sent: Friday, February 07, 2014 12:23 AM
Subject: Re: [RFMRI] correlation matrix
 
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]
 
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: http://www.rfmri.org/comment/3026#comment-3026


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

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
 
 
Sent: Monday, February 10, 2014 6:35 AM
Subject: Re: [RFMRI] correlation matrix
 
[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: http://rfmri.org/comment/3029#comment-3029


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
 
 
 
Sent: Saturday, February 15, 2014 4:53 AM
Subject: Re: [RFMRI] correlation matrix
 
[To post a comment, please reply to rfmri.org@gmail.com ABOVE this line]
 
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: http://rfmri.org/comment/3032#comment-3032


 

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

Hi, image is uploaded.

tetsuya

This is the first column of ROISignal.mat

0
0
0
0
0
0
-0.686671256552476
-0.902382223255756
-0.690875177251507
-0.782266318780029
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.481744829168931
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.792505461311762
-0.622489104326792
-0.411062812871129
-0.249033350201067
0.158523925271366
0.718787582975790
1.05873182875327
1.05075960001860
1.05075960001860
1.05075960001860
1.05075960001860
1.05075960001860
1.05075960001860
1.05075960001860
1.05075960001860
0.734288697570600
0.734288697570600
0.734288697570600
0.734288697570600
0.734288697570600
0.734288697570600
0.734288697570600
0.734288697570600
1.05847386751530
1.34353133712819
0.759711836673979
0.0947104694894995
-0.675486944211105
-0.954582472616179
-0.954582472616179
-0.954582472616179
0.554173746808062
0.554173746808062
0.554173746808062
0.554173746808062
0.496361922629899
0.213780714581144
0.548942916330126
1.09362019974308
1.42148738878540
2.07235732213014
1.55745112442625
1.55745112442625
1.55745112442625
0.547813990284283
0.547813990284283
0.547813990284283
1.10954900780183
1.88831705897715
1.88831705897715
1.88831705897715
1.88831705897715
0.228706830369868
0.228706830369868
0.228706830369868
0.228706830369868
0.534491579343338
2.01517245110604
3.05960767772695
3.05960767772695
3.05960767772695
-0.656517132756265
-0.656517132756265
-0.656517132756265
-0.656517132756265
-0.656517132756265
-0.656517132756265
-0.656517132756265
-0.656517132756265
-0.656517132756265
-0.656517132756265
-0.656517132756265
-0.0894060240032927
-0.0894060240032927
-0.0894060240032927
-0.0894060240032927
-0.0894060240032927
-0.0894060240032927
-0.0894060240032927
-0.0894060240032927
-0.0894060240032927
0.493579415451606
1.43132945683926
2.61822179391534
3.50626900457779
3.57797445795147
3.57797445795147
3.57797445795147
3.57797445795147
3.57797445795147
3.57797445795147
3.57797445795147
3.57797445795147
3.57797445795147
3.57797445795147
3.57797445795147
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
-2.80515385059851
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
1.48807052648599
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.823221824408676
0.458969114091001
0.128098422467776
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
 

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

Permalink

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
 

Forums
DPABI/DPABISurf/DPARSF