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I'm trying to use the EMSegment Command-line Interface to segment several brain MRI cases with atlas. I'm using MRI-Human-Brain-Full-Parcellation.mrml as the MRML scene defining the task and EM_Map.nrrd as the result labelmap. I wish to add several target volumes at once (to avoid running the EMSegmenter with Atlas module for each case) but it is not allowing me to do so. The documentation at http://www.slicer.org/slicerWiki/index.php/Modules:EMSegment-Command-Line3.6 explains that multiple files can be selected at once. Is this not possible anymore for the 4.5 version of Slicer? If so, what other options do I have to run the segmentation in a batch of cases?
Also, when I tried running the module with one target volume, the status was 'completed with errors'. The error shown in the log was 'MetaImage: Read: Cannot open data file.' The EMSegmenter with Atlas module could open .mhd files, I assumed it would be the same for the Command-Line Interface. Do I need to first convert the file to a .nrrd format?