Hi Yasmine,
If you manage to select the region you want to delete (by getting a binary "mask" version of it as Rosalina described), you're also then very close to being able to remove it from the intital atlas.
If you apply the -binv flag from fslmaths to that binary mask, you'll then get an "inverted" version of it; i.e. a version of it where every pixel which isn't part of that region is a "1", and every bit which is is a "0".
If you then use fslmaths to multiply the original atlas by that "inverted" mask, the resulting image will be the original atlas but with the region you extracted removed (all those pixels set to "0").
Iain
