[RFMRI] basic question on graphvar input data

Submitted by paban on

Johann Kruschwitz

Thu, 04/16/2015 - 10:18

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Hi Veronique,

welcome to the "graph-theoretical-world"! For getting startet I would suggest to read some literature as:

Complex network measures of brain connectivity: Uses and interpretations


1.)  you cannot enter .nii images into GraphVar. A crucial step would be to first "define" the nodes of your graph by extracting the time-series signals from the regions of interest that you are interested in (e.g. aal-atlas or any other ROIs). For this step I would suggest to use DPARSF (as the extraction output directly fits to the demands of GraphVar). Please refer to the DPARSF online course (http://rfmri.org/Course) for how to do that. Please also have a look in the GraphVar sample workspace/data where there are templates of how the data input should look like.

It would also be important to read some papers about how to preprocess your data for reliable graph theoretical analyses:

Test-retest reliability of resting-state connectivity network characteristics using fMRI and graph theoretical measures.


2.) conn matrix refers to "connectivity matrix". If you create the conn matrix with your time-series signals, it will automatically be loaded into the subject list. Alternatively you could use the ready output connectivity matrices from DPARSF (although you will have more possibilies when generating the conn matrix with GraphVar). As mentioned above please have a look at the required format of the conn matrices in the sample workspace.

I hope this helps,

Johann

Thank you very much for your quick reply. I know the papers that you refer to …. my problem  concerns more the practical aspects in the use of the toolbox than its philosophy ! Let me try DPARSF before I request new help !

Veronique,

 

De : RFMRI.ORG [mailto:rfmri.org-bounces@rnet.co] De la part de The R-fMRI NetworkEnvoyé : jeudi 16 avril 2015 12:18
À : rfmri.org@rnet.co
Objet : Re: [RFMRI] basic question on graphvar input data

 

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

 

Commented by Johann Kruschwitz (Johann Kruschwitz)

Hi Veronique,

welcome to the "graph-theoretical-world"! For getting startet I would suggest to read some literature as:

Complex network measures of brain connectivity: Uses and interpretations


1.)  you cannot enter .nii images into GraphVar. A crucial step would be to first "define" the nodes of your graph by extracting the time-series signals from the regions of interest that you are interested in (e.g. aal-atlas or any other ROIs). For this step I would suggest to use DPARSF (as the extraction output directly fits to the demands of GraphVar). Please refer to the DPARSF online course (http://rfmri.org/Course) for how to do that. Please also have a look in the GraphVar sample workspace/data where there are templates of how the data input should look like.

It would also be important to read some papers about how to preprocess your data for reliable graph theoretical analyses:

Test-retest reliability of resting-state connectivity network characteristics using fMRI and graph theoretical measures.


2.) conn matrix refers to "connectivity matrix". If you create the conn matrix with you r time-series signals, it will automatically be loaded into the subject list. Alternatively you could use the ready output connectivity matrices from DPARSF (although you will have more possibilies when generating the conn matrix with GraphVar). As mentioned above please have a look at the required format of the conn matrices in the sample workspace.

I hope this helps,

Johann


Online version of this post: http://www.rfmri.org/comment/3661#comment-3661

 

Hi, I am new in this “graph-theoretical word”, so please forgive me for my stupid question (and also for my bad English … I am French actually!!). Well, GraphVar seems to be a very good tool…. I will just have to hit some buttons, that is good for me !! However, 1) I have problem starting at the first step. Indeed, in the manual, it is indicated that it is possible to create connectivity matrix with the toolbox. To do this, I have “to select time series signals for each subject” ….. what that’s mean ? do I have to select the 245 XX.nii files created from SPM for each subject ? 2) in “select subjects (conn Matrix)” what is “conn matrix” ? is there any relationship with CONN toolbox ?. In addition, is it possible to use correlation matrix generated from CONN toolbox ? Thank you for your help, Veronique De : RFMRI.ORG [mailto:rfmri.org-bounces@rnet.co] De la part de The R-fMRI Network Envoyé : mercredi 15 avril 2015 17:10 À : rfmri.org@rnet.co Objet : Re: [RFMRI] error about graphvar [To post a comment, please reply to rfmri.org@gmail.com ABOVE this line] Commented by Johann Kruschwitz (Johann Kruschwitz) Hi, please highlight the subject name again and check if the number in the "Start" field changes from 21 to 12 (as I see in your screenshot it is 21). 12 should be the starting character and End 4. If for some reason it does not work properly when using the mouse you can alternatively enter the starting and end character manually. Hope it works now! Johann Online version of this post: http://rfmri.org/comment/3660#comment-3660 Many a little makes a mickle -- your kind contributions shall make our efforts not perish from the earth. Please help The R-fMRI Network at http://rfmri.org/#overlay=HelpUs To manage subscriptions, please visit: http://rnet.co/mailman/listinfo/rfmri.org_rnet.co Mail comment ID: http://rfmri.org/mailcomment/redirect/%3C31.2003.3660.1429110596.caa82bdab3ee69877423a4cb2559a2cc%40www.rfmri.org%3E