Are you installing MCR in non-standard location? If yes, please set BrainSuiteMCR environment variable to point to the path. You can do that in Linux by
export BrainSuiteMCR=/path/to/your.mcr
Please make sure that the atlas is unzipped into a folder and copied to the svreg subfolder within BrainSuite installation. It needs to be along with other atlases within svreg subfolder.