To create label volumes and label index files from Amira label files for use in SHIVA and MBAT:

To generate the label image, in Amira, save label file label file as Analyze Image. Be aware that Amira does not record the orientation of images so that the images volumes may need to be flipped to match image volumes. 

Label index files (.lbl) are generated using Analize Labeler Plugin. To use, put Plugin into ImageJ Plugin directory/folder. Launch ImageJ; select Plugins->Analize Labeler. A standard "open file" window opens titled "Amira file". Navigate to the Amira label file to be extracted and select. Label index file is written using the name of the Amira file with .lbl extension.