I have a single subject data(T1w and rs-fMRI BOLD). I am wanting to generate functional connecitivty matrix after preprocessing the raw fMRI. I already used CONN toolbox to do the entire preprocessing. I have now completed the first-level analysis as well.

Since I am wanting to calculate FC matrix, I have computed ROI-to-ROI connectivty during first-level analysis. I belieive this is the correct way forward. I am having the output file named "resultsROI_Subject###_Condition###.mat". Can someone please show me how to compute FC matrix values using this file.

I am extracting 'Z' values from "resultsROI_Subject###_Condition###.mat". I am then calculating correlation coefficients of Z using MATLAB 'corrcoef' function. So the resultant matrix that I get after doing this MATLAB operation, is it the FC matrix that I want?

Here is the Z matrix obtained after running CONN preprocessing pipeline. Z is of size (RoI$\times$RoI). Here, the number of RoI is 105. Z represents Fischer-transformed correlation coefficient between each source and target RoI.

Z matrix - 105x105

Here is the result after applying MATLAB tanh function. MATLAB code -> Z_tanh = tanh(Z);


  • $\begingroup$ I haven't used that specific toolbox, but is this not covered at web.conn-toolbox.org/tutorials ? $\endgroup$
    – Bryan Krause
    Jul 5, 2019 at 19:37
  • $\begingroup$ No, its not given there. $\endgroup$
    – zoozoo
    Jul 6, 2019 at 8:41
  • $\begingroup$ Given that FC is kind of the bread and butter of fMRI I am skeptical you should need to do this manually with a distributed package... $\endgroup$
    – Bryan Krause
    Jul 6, 2019 at 9:01
  • $\begingroup$ I've been talking behind the scenes with other mods. Across the SE network we kind of lack the expertise in this field. Another mod suggested you 'computerize' your Q and enter some code and some outputs so people can have more insight in the code issues. Even then it may not be answerable, but then we could migrate it to another site for you with more computer science experts. $\endgroup$
    – AliceD
    Jul 6, 2019 at 11:22
  • $\begingroup$ Added matrix visualizations and MATLAB function for transformation. $\endgroup$
    – zoozoo
    Jul 9, 2019 at 9:15


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