I am new to fMRI. I am working on a QSM analysis. I am trying to find a way to take a susceptibility map and apply ROIs to the map (this I already know how to do) but only look at the gray matter voxels. The susceptibility values we are getting are coming out with negative values, but we are only looking at deep gray matter regions (these should all be positive). The ROIs are including some of the surrounding white matter (which has a negative susceptibility value), so we want to eliminate this issue. I have tried using FAST to segment the brain and add this to the susceptibility map prior to overlaying the ROIs, but it was not working for me. If anyone has an idea of how to do this, including what fsl commands to use to achieve our desired results, it would be much appreciated!