When I run a command line module and there is a missing argument the error about the missing arguments are illogical. For instance when I run  edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion with no arguments the output is 

Could not find library, using working directory /home/local/VANDERBILT/plassaaj/jist-lib
cli ####################################################################
cli Initializing MIPAV/JIST Framework
cli ####################################################################
cli Interpretting command line arguments
cli ####################################################################
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion
inAtlas = =
inTarget = = Target Image Volume
inAtlas2 = =
inHierarchy = = None
inProbability = = None
inOutput = = None
inOutput2 = = None
inConsensus = = 0.99
inPrior = = Voxelwise
inConvergence = = 1.0E-4
inMaximum = = 100
inWindow = = 5
inWindow2 = = 5
inWindow3 = = 5
inWindow4 = = 0
inBias = = 0
inAugment = = false
inWeighting = = MSD
inSearch = = 3
inSearch2 = = 3
inSearch3 = = 3
inSearch4 = = 0
inPatch = = 2
inPatch2 = = 2
inPatch3 = = 2
inPatch4 = = 0
inSearch5 = = 1.5
inSearch6 = = 1.5
inSearch7 = = 1.5
inSearch8 = = 1.5
inDifference = = 0.25
inGlobal = = 0
inLocal = = 0.1
inUse = = true
inSelection = = Jaccard
inSelection2 = = 0.05
inNumber = = 150
outLabel = = Label Volume
outPerformance = =
outPerformance2 = = Performance Level Parameters Volume
outLabel2 = =
outLabel3 = = Label Probabilities Volume
outProc = /fs1/masi/plassaaj/MSSTAPLE/DeepBrainSegmentation
cli ####################################################################
Module Failed in an Ungraceful Manner. Please contact the developer with the following message.
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusionRuntime Exception:0
edu.vanderbilt.masi.algorithms.labelfusion.ObservationBase.determine_cropping_information(ObservationBase.java:328)
edu.vanderbilt.masi.algorithms.labelfusion.ObservationVolume.(ObservationVolume.java:28)
edu.vanderbilt.masi.algorithms.labelfusion.ObservationVolume.(ObservationVolume.java:14)
edu.vanderbilt.masi.plugins.labelfusion.AbstractStatisticalFusionPlugin$AbstractExecuteWrapper.get_observation_type(AbstractStatisticalFusionPlugin.java:459)
edu.vanderbilt.masi.plugins.labelfusion.AbstractStatisticalFusionPlugin$AbstractExecuteWrapper.execute(AbstractStatisticalFusionPlugin.java:348)
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion.execute(PluginStatisticalFusion.java:66)
edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:337)
edu.jhu.ece.iacl.jist.pipeline.ProcessingAlgorithm.runAlgorithm(ProcessingAlgorithm.java:321)
edu.jhu.ece.iacl.jist.cli.run.main(run.java:100)
edu.jhu.ece.iacl.jist.pipeline.CalculationMonitorCalculation monitor shutting down by interrupt.
---------- Performance Summary ----------
1) Algorithm Calculation -- ELAPSED TIME: Actual: 0.02 sec / CPU: 0.01 sec

TOTAL ELAPSED TIME: Actual: 0.02 sec / CPU: 0.01 sec
CURRENT MEMORY: Used 28 MB, Free 332 MB, Total 361 MB
cli ####################################################################
cli Done: edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion
cli ####################################################################

Which says the error is the developer's fault. Inherently this is true in that the cli does not validate the inputs at all, but this error implies that the module developer is at fault.

Hi Andrew,

I just pushed a fixed for this. There was a minor bug in the CLI. I also started a new public build if you are eager to try. Here's the new output of running the same command:

cli ####################################################################
cli Initializing MIPAV/JIST Framework
cli ####################################################################
cli Interpretting command line arguments
cli ####################################################################
edu.vanderbilt.masi.plugins.labelfusion.PluginStatisticalFusion
PARSE ERROR: Missing required tag: inAtlas
inAtlas = =
inTarget = = Target Image Volume
inAtlas2 = =
inHierarchy = = None
inProbability = = None
inOutput = = None
inOutput2 = = None
inConsensus = = 0.99
inPrior = = Voxelwise
inConvergence = = 1.0E-4
inMaximum = = 100
inWindow = = 5
inWindow2 = = 5
inWindow3 = = 5
inWindow4 = = 0
inBias = = 0
inAugment = = false
inWeighting = = MSD
inSearch = = 3
inSearch2 = = 3
inSearch3 = = 3
inSearch4 = = 0
inPatch = = 2
inPatch2 = = 2
inPatch3 = = 2
inPatch4 = = 0
inSearch5 = = 1.5
inSearch6 = = 1.5
inSearch7 = = 1.5
inSearch8 = = 1.5
inDifference = = 0.25
inGlobal = = 0
inLocal = = 0.1
inUse = = true
inSelection = = Jaccard
inSelection2 = = 0.05
inNumber = = 150
outLabel = = Label Volume
outPerformance = =
outPerformance2 = = Performance Level Parameters Volume
outLabel2 = =
outLabel3 = = Label Probabilities Volume
outProc = /home-nfs/local/VANDERBILT/damons/workspace/JIST Plugins
cli ####################################################################
cli Exiting with errors.

Cheers,
Steve