help! how to extract brain subcortial

how to extract brain subcortial use altas to create multi rois with command line (FSL not frst ,because just 7 part? no Freesurfure because too long).
I try to use this founction :http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg_Segmentation_Propagation_Tutorial,but it did not seg the subcortial

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