If I understand what you mean correctly, this should do it:
tckmap your_tracks.tck -template your_inclusion_ROI.mif - | mrcalc - your_inclusion_ROI.mif -mult final_map.mif
Essentially: use tckmap to create an image of streamline counts for your tracks in ROI space, then multiply that by your ROI image itself. Is this what you were after?