GraphVar

Dear users,

I have started to use GraphVar, though am still learning all of the functions.

I was able to follow the tutorial, but am now running into some difficulties using some of my own 'practice' data of 5 participants.

I have used ExploreDTI to create some connecitivty matrices. ExploreDTI does not output the matrices in the correct format required for GraphVar, whereby the main diagonal may not always equal to '0'. I have, therefore, changed all main diagonal elements to equal '0'.

Hii all,

I would like to know more about SICE method. In GraphVar I am using following procedure for creating connectivity matrices from time series.

Using time series of fmri images I want to create connectivity matrix of particular SICE target density (0.25-0.45) with an increment of 0.05.  I would like to know more about SICE target density. Does it means, say 0.25 target density means 25 percent of your connections are retained or not?.

Pls help me to clear this doubt.

Thanks,

Mini

Hi all,

I am using GraphVar for deriving network measures in an rsfmri study. I would like to know the number of null model network required for a particular rewiring algorithm.

eg:- In my study I am using rewiring alogorithm 'randmio_und' and from literature review I came to know that the default value for null model network is 20 and it will vary aaccording to the algorithm you are using. Anybody have idea regarding this. If so pls help me out.

Thanks,

Mini

Hi, 

I got the following errors during running "Calculate variables and export". I would appreciate if you could help me fix these errors.

Hello

When I try to run the "Network Calculations" section of GraphVar by clicking on the "Calculate variables and export" button, it seems to do the calculating just fine, but then gives this error (copied below) when it goes to export.  I haven't had any problems with the Statistics or correlations portion on this dataset, just this section for basic network calculations.  It doesn't seem to matter what metric I'm using.

I've included a screenshot of the things that I've selected in the GUI.

Thanks!

Hello.

I was wondering if I can generate ROI signals using either fsl or AFNI for GraphVar.

Thanks,

Yuko

I'm trying to use a 24 node network, and I'm having trouble getting my brain regions file to load.  When I try to use anything except the default AAL 119 regions, I get an error (which I've copied below).  I also attached the file that I'm trying to load in.

Dear GraphVar users,

I would like to run an analysis with NBS in GraphVAR. I use to run NBS with the NBS1.2 toolbox in SPM8. I am a little confused with the different options in GraphVar. Could someone help me? I attach a capture of my workspace to see you the options I have chosen.

Can someone explain to me how to choose the threshold t as in NBS1.2?

Where can I choose the number of permutations? Is it in the "number of repetition" part of the workspace?

Thanks for your help,

All the best,

Cha

Hi, I have some questions about the results from an NBS analysis on raw connectivity matrices. For questions, we could look to the example NBS table in the manual (attached).

1. Could you expland on exactly how (i.e., equation or formula) the alpha value in the 5th column is calculated? I'm having trouble figuring this out from the NBS papers. e.g., is the alpha derivable from the other columns in the network inspector table?  

Dear GraphVar users,

I have some problems with my data. As explained in the tutorial, I have created two files one for Brain regions and one for my variables. I have 78 ROIS and 44 subjects (22 controls and 22 decliners). When I load my xls or my csv files I have an error message:

Error using xlsread (line 247)Subscript indices must either be real positive integers or logicals.

If I change something in the file, i have this error message: Error using xlsread (line 247)Index exceeds matrix dimensions.