I don't know exactly what "fill the black region in the region of Interests" means. If you want to fill the black regions with black, thus making the white "islands" or "holes" black also (essentially making them disappear), then use bwareafilt() and specify the smallest white blob that you're willing to accept. For example, if you want to remove all blobs smaller than 1000 pixels, do this:
binaryImage = bwareafilt(binaryImage, [1000, inf]);
You could also use bwareaopen().
binaryImage = bwareaopen(binaryImage, 1000);
On the other hand, if you want to remove black holes in white regions, simply use imfill:
binaryImage = imfill(binaryImage, 'holes');
I also don't know what the "region of interest" is in that image. Can you indicate it, perhaps by outlining it in red? If the ROI is only part of the whole image, then you'll need to make a mask somehow, perhaps with poly2mask() or some other method depending on how ROI is defined, then use the mask to erase the non-ROI parts of the image.
binaryImage(~ROIMask) = false;