I am inputting a probabilisitic MNI-space left amygdala .nii mask in the set-up phase and am curious if it would be helpful to also mask that small volume using "Select "mask with grey matter" on selected ROIs to further restrict these ROIs' voxels to those voxels within the estimated grey matter mask for each subject."

If I do mask this MNI-space ROI for each subject, should I also select the box for 'Subject-specific ROI'?

I ask because  when reviewing the QA plots for successful co-registration of the ROI with the participant's structural/functional, I only see 1 amygdala ROI but there are 28 subjects. Is CONN masking the ROI with one participants GM mask and then applying that amygdala seed to the other participants?

Thanks!
Sarah