Hi everyone,

I’m trying to run second-level analyses in CONN, but I’ve run into some confusion and would really appreciate some guidance.

I’ve already completed my first-level analyses using the TMFC toolbox. This gave me ROI-to-ROI connectivity matrices (not z-scores, but subject-level beta/contrast estimates) for different task conditions. So for each subject and condition, I have a full connectivity matrix (ROI × ROI).

My goal is to take these matrices and perform second-level analyses in CONN, specifically:

• 
  

  Seed-based ROI-to-ROI analysis using the NAcc as seed (left and right separately)

  
  


• 
  

  Group comparisons 

  
  


• 
  

  Regressions with clinical variables

  
  


• 
  

  Across multiple condition contrasts (e.g., condition A > condition B,  etc.)

  
  

I tried to integrate these outputs into CONN by using a script with functions like conn_mtx_write to format my matrices into .mtx.nii files, assuming this might allow CONN to treat them as first-level inputs for second-level analysis.

However, I’m not fully sure how to correctly define and use the NAcc (left and right) as seeds in this setup. Is there a code template or similar?

I would really appreciate any advice or examples of how to properly set this up.

Thanks a lot in advance!