Combine ROIs using MarsBaR - mind-lab-bos/MBI_Project_MRI_Analysis GitHub Wiki

We have a set of default CONN atlas files saved in /work/mindlab/ROIs/CONN_Atlas/Atlas/ (the files are all zipped, you would need to unzip them before use). The auditory and reward ROIs are saved in /work/mindlab/ROIs/Wang_etal_ROIs/.

Open a Matlab session on Discovery.

Type the following lines of code in command window:

addpath('/work/mindlab/Programs/spm12')

addpath('/work/mindlab/Programs/spm12/toolbox/marsbar')

marsbar

The fish will pop up. That's MarsBaR.

  1. First we need to convert those .nii files into .mat files for MarsBaR to read (Eva has done this for all CONN atlases and saved the mat files in the /work/mindlab/ROIs/CONN_Atlas/Atlas/mat/ folder). We can do so by running this script /work/mindlab/ROIs/ROI_nii2mat.m or manually by following these steps:

ROI Definition -> Build

Type of ROI -> Image

Select the ROI .nii file you'd like to import

Maintain as binary image -> No Apply function to image -> No Description & Label for ROI: no need to change, just press enter

Select a folder to save the new .mat file

Do this for other ROIs you'd like to import.

  1. Combine ROIs

ROI Definition -> Transform

Transform:... -> Combine ROIs

Function to combine ROIs: r1+r2 (can change function if you'd like to do other things to these ROIs)

Select a folder to save the .mat file for the new combined ROI

  1. Export the ROIs into .nii (these settings apply when you'd like to keep it consistent with other default ROIs in CONN)

ROI Definition -> Export

Export ROI(s) to:... -> image

Choose "Base space for ROIs"

Select a folder to save the new .nii file. Now this new ROI is ready to be imported into CONN.