Extract brain ROIs and build functional connectivity matrix of ADNI dataset

Hello everyone,

I’d like to extract brain ROIs, time series and estimate correlation matrices from ADNI dataset which are 3D nii images.

Thank you so much


There are a few option you can use for this: The CONN Toolbox (has a GUI so is a bit more user friendly), FSL Feat (more easily scriptable), and XCPEngine (also scriptable, modular using multiple softwares).

Some considerations to guide your choice:

  1. How comfortable are you scripting? If not so much, then I recommend CONN.
  2. How did you preprocess your data? If you used fMRIPrep, both CONN and XCPEngine have compatibility with it .
  3. Do you know what kind of ROIs you want, as in what atlas they come from? CONN has the Harvard-Oxford cortical atlas built in, which is convenient.
  4. How many subjects? CONN is probably the least scalable out of the three options, in that it gets more unwieldy to use with a high number of subjects.

These are just a few things to keep in mind. Hope this helps!


Hi @Steven

Thank you so much for reply. I’ve tried FSL but I got error when I use my dataset. I’m ok with scripting. I’m using nilearn package and I’ll try to use HO atlas. Also, I’ll try to use either CONN or XCOEngine.

Warm Regards