If I remember correctly, the atlas list should contain the names of a group of T1 images and corresponding binary masks that have been modified to include only brain tissue. These images will be registered to your input scan to create a probability mask, basically using info from the atlas volumes to inform segmentation of brain from dura and other intracranial structures. It should be included in TOADS-CRUISE, but you can also download the atlas and text file here: http://www.nitrc.org/frs/?group_id=271 (save the file named SPECTRE_ATLASES-v2.tar.gz, as the others do not seem to work). When SPECTRE asks for an atlas file, point it to the text file and corresponding directory of atlas images.

I hope that helps!

Jen