Hi Wes, For correct computation of ROI-wise statistics, the hand-drawn labels should overlay correctly with *.bfc.nii.gz file in BrainSuite GUI.
In order to achieve that you can co-register the anatomical image (converted to .nii) on which the labels were drawn to the *.bfc.nii.gz file generated by BrainSuite. This registration should be done in rigid fashion, with 6 DOF, and following registration tool can be used for the purpose:
http://neuroimage.usc.edu/neuro/Resources/BDPAddons#affineReg
Next, you should apply the same transformation to the hand-drawn label file itself (converted to .nii) using transform_data_affine() function with ‘nearest’ interpolation method. Please see the html file in the registration-tool zip/folder for detailed documentation.