Hi everyone,

I’m an intern and this is my first time working on functional connectivity analyses. I’m trying to prepare inputs for the NBS toolbox using gPPI matrices from the TMFC toolbox (https://github.com/Masharipov/TMFC_toolb...), and I’m a bit unsure if I’m doing it correctly. I’ve followed the NBS manual, but as a beginner, some parts aren’t very clear.

Here’s what I’ve done so far: I wrote a MATLAB script to process the subject-level ROI-to-ROI gPPI matrices and create NBS input files. I also wanted to include covariates like symptom scores (MADRS, STAI-S, STAI-T, SHAPS) and group (healthy controls, HC vs high symptom group, HS). Previously, I only used the TMFC toolbox, which outputs matrices for each subject for a specific contrast/condition (in my case it's just condition A), but with TMFC I can’t include covariates or group information.

The input files created:

1. 
   

   Subject matrices:

   
   
   
   
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     Stored in a mat file (size: [nROIs x nROIs x nSubjects])

     
     
   
   
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     Each slice along the 3rd dimension is a symmetric ROI-to-ROI connectivity matrix for one subject 

     
     
   
   
   
   
   
2. 
   

   Node labels:

   
   
   
   
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     txt file which contains the list of ROIs corresponding to the rows/columns of the matrices.

     
     
   
   
   
   

    

   
   
   
3. 
   

   Design matrix:

   
   
   
   
   • HERE I AM REALLY UNSURE
   
   
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     Size: [nSubjects x 7]

     
     
   
   
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     Columns: intercept (a column of 1s) , HC dummy, HS dummy, MADRS z-score, STAI-S z-score, STAI-T z-score, SHAPS z-score.

     
     
   
   
   
   
   
4. 
   

   Contrasts:

   
   
   
   
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     contrast_full_HS_HC.txt: HS vs HC comparison

     
     
   
   
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     contrast_full_MADRS.txt, contrast_full_STAI_S.txt, contrast_full_STAI_T.txt, contrast_full_SHAPS.txt: each testing the association with a single covariate

     
     
   
   
   
   
   

My questions:

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  Does this workflow look correct for preparing NBS inputs from gPPI matrices?

  
  


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  Are all of the created files correct?

  
  


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  Is it okay to include covariates and group this way, or am I missing something important?

  
  


• What statistical test should I choose? I chose t-test so far ?


• I am using FDR, so how many permutations should I use? 

Any guidance or tips would be greatly appreciated, especially since I’m quite new to this. Thanks in advance!