FSL has a very useful feature of creating and applying masks easily to large number of images. The first step is to create a mask. FSL-eyes provides one method to do that, but I would not go in to details of it. Another method to create masks is by indicating the coordinates of the region of interest and defining the radius, in pixels, of the circle around it. Below are quick commands to do that

 

 

 

 

Once the mask is created, one can easily apply it to the desired image using the following command

 

 

 

 

An important tip if you are making masks using FSLeyes. Don’t close your FSLeyes in which you are editing your mask until and unless you are completely satisfied with your mask results. If is much easier to edit your mask if the original file is still open.