AAL116 atlas for determining the ROIs

Hello Everyone,

I am trying to determine the ROIs using the AAL116 atlas. I want to use the ROIs as nodes when doing tractography using 3dTrackID in AFNI.

I used GRETNA for the rs-fMRI data and the AAL116 atlas was used to determine the ROIs in the background.

Could you please advice or guide me how to do the same for the structural data.

This is my approach thus far:

Linear and non-linear registration of T1 to MNI space using flirt and fnirt (from FSL) respectively.
Then inverse the non-linear transformation and warp the parcellated ROIs back to T1.

The questions I have are:

  1. Do I need to make a mask for each 116 ROIs and warp them to T1 individually or can I warp the entire atlas with all the ROIs to T1 once and then use that for tractography?
  2. The netrois input in the 3dTrackID command wants laballed regions - how do I obtain this?

If you have any resources that have guidelines and steps on how to use the atlas that would be much appreciated.

Thank you so much.

Kind regards,