Create a mask from an image with gap edges

Ok the illustration below sums up what I need to do. I have a picture of a brain, I have segmented but it keeps giving gaps in edges probably due to the image being unclear. So I have patched up the gaps with red (probably imfreehand), and then I need to fill up the brain to create a mask. This is proving hard as imfreehand needs to go "around" the whole structure, if you read below you will understand.

I cant imfreehand around the whole brain because the teacher said its (original brain structure) is too complicated and the teacher wants a semi automatic method, at worst fill in the gaps but not spend all day outlining the brain thats easy but also tedious. If you get what I mean.

I have to create 1000s of masks of a 3d volume hence the need for something a bit quicker.

Cheers