How can I get the coordinated in NifTi-files?

Hey guys,

I work on NifTi-files (fMRI images) running them in MRIcron in order to find the corrdinates of reions of interest (Activated regions). Then I transfer these coordinated to another Matlab program to calculate the Hemodynamic responses.

The problem is with finding the coordinates since I have do click on voxels one-by-one and write the related coordinated. As you might already have realized this method is so painful and time consuming. i would like to find a way that, for instance, I can define the whole region of interest (let's say by masking or any other way) and then find the entire coordinates that are already included in the mask.

Using this method will save my time.

In advance, I would be so grateful for your help.

Mehdi