Some CLI modules when called with -xml flag return XML that is not well formed. This is due to tags to a I think they should be replaced by  or and parsed appropriately (those tags use commas not semicolons). Here are some of the affected plugins:

• de.mpg.cbs.jist.tools.JistToolsMultiCropToROI
• de.mpg.cbs.jist.tools.JistToolsComposeTransMatrices
• de.mpg.cbs.jist.modules.JistModuleComposeTransMatrices
• de.mpg.cbs.jist.modules.JistModuleLevelsetAppearancePCA
• de.mpg.cbs.jist.modules.JistModuleBatchImageCalculator
• de.mpg.cbs.jist.modules.JistModuleLevelsetPCASegmentation
• de.mpg.cbs.jist.modules.JistModuleCopyData
• de.mpg.cbs.jist.modules.JistModuleMipavFullReorient
• de.mpg.cbs.jist.modules.JistModuleRescaleVolume
• de.mpg.cbs.jist.modules.JistModuleLevelsetPCAApproximation
• de.mpg.cbs.jist.modules.JistModuleCorticalProfileGeometry3
• edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT
• de.mpg.cbs.jist.modules.JistModuleCopyData
• edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask

edu.jhu.ece.iacl.plugins.registration.MedicAlgorithmFLIRT and edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask now work. I opened up a tracker on the CBS page here: https://www.nitrc.org/tracker/?func=deta... about the remaining 3 that do not generate the schema.

Tested out v3.0.2 of the CBS tools with the most recent JIST Build. Below is a list of the current packages:

• de.mpg.cbs.jist.surface.JistSurfaceProbabilityToLevelset
• de.mpg.cbs.jist.surface.JistSurfaceLevelsetToMesh
• de.mpg.cbs.jist.surface.JistSurfaceLevelsetToProbability
• de.mpg.cbs.jist.surface.JistSurfaceTrackingLevelsetInflation
• de.mpg.cbs.jist.surface.JistSurfaceMeshDataToLevelset
• de.mpg.cbs.jist.surface.JistSurfaceMeshToLevelset
• de.mpg.cbs.jist.surface.JistSurfaceLevelsetReinitialization
• de.mpg.cbs.jist.surface.JistSurfaceMeshToRescaledLevelset
• de.mpg.cbs.jist.surface.JistSurfaceLabelFileToVolume
• de.mpg.cbs.jist.surface.JistSurfaceLevelsetToTarget
• de.mpg.cbs.jist.surface.JistSurfaceMgdmRepresentation
• de.mpg.cbs.jist.filter.JistFilterTubularStructures
• de.mpg.cbs.jist.filter.JistFilterRidgeStructures
• de.mpg.cbs.jist.brain.JistBrainMp2ragePVFilter
• de.mpg.cbs.jist.brain.JistBrainFilterStacking
• de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping
• de.mpg.cbs.jist.brain.JistBrainExtractBrainRegion
• de.mpg.cbs.jist.brain.JistBrainMp2rageArteriesFilter
• de.mpg.cbs.jist.brain.JistBrainMgdmSegmentation
• de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation
• de.mpg.cbs.jist.brain.JistBrainMgdmMultiSegmentation2
• de.mpg.cbs.jist.brain.JistBrainMgdmMultiSegmentation
• de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter
• de.mpg.cbs.jist.statistics.JistStatisticsLesions
• de.mpg.cbs.jist.statistics.JistStatisticsSurface
• de.mpg.cbs.jist.statistics.JistStatisticsSegmentation
• de.mpg.cbs.jist.statistics.JistStatisticsTimeSeries
• de.mpg.cbs.jist.utilities.JistUtilitiesRenameImage
• de.mpg.cbs.jist.utilities.JistUtilitiesCopyData
• de.mpg.cbs.jist.utilities.JistUtilitiesCropToROI
• de.mpg.cbs.jist.utilities.JistUtilitiesImageBoundary
• de.mpg.cbs.jist.utilities.JistUtilitiesCopyHeader
• de.mpg.cbs.jist.utilities.JistUtilitiesCropToDimensions
• de.mpg.cbs.jist.intensity.JistIntensityBackgroundEstimator
• de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking
• de.mpg.cbs.jist.intensity.JistIntensityWeightedCombination
• de.mpg.cbs.jist.intensity.JistIntensityRangeNormalization
• de.mpg.cbs.jist.intensity.JistIntensityBounds
• de.mpg.cbs.jist.intensity.JistIntensityCombinations
• de.mpg.cbs.jist.intensity.JistIntensityFlairFiltering
• de.mpg.cbs.jist.segmentation.JistSegmentationSmoothProbabilityMap
• de.mpg.cbs.jist.segmentation.JistSegmentationProbabilityExtraction
• de.mpg.cbs.jist.segmentation.JistSegmentationProbabilityCombination
• de.mpg.cbs.jist.segmentation.JistSegmentationFitMgdmEdges
• de.mpg.cbs.jist.segmentation.JistSegmentationMgdmAdjust
• de.mpg.cbs.jist.segmentation.JistSegmentationRefineMgdm
• de.mpg.cbs.jist.segmentation.JistSegmentationRelabel
• de.mpg.cbs.jist.cortex.JistCortexCentralSurface
• de.mpg.cbs.jist.cortex.JistCortexACE
• de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshInflation
• de.mpg.cbs.jist.cortex.JistCortexMyelinatedThickness
• de.mpg.cbs.jist.cortex.JistCortexSmoothData
• de.mpg.cbs.jist.cortex.JistCortexFullCRUISE
• de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshMapping
• de.mpg.cbs.jist.cortex.JistCortexExtractionCRUISE
• de.mpg.cbs.jist.fmri.JistFmriCorticalSmoothing
• de.mpg.cbs.jist.laminar.JistLaminarROIAveraging
• de.mpg.cbs.jist.laminar.JistLaminarProfileSampling
• de.mpg.cbs.jist.laminar.JistLaminarProfileCalculator
• de.mpg.cbs.jist.laminar.JistLaminarVolumetricLayering
• de.mpg.cbs.jist.laminar.JistLaminarProfileGeometry
• de.mpg.cbs.jist.registration.JistRegistrationSurfaceMeshGroupAverage
• de.mpg.cbs.jist.registration.JistRegistrationMultimodalSurface
• de.mpg.cbs.jist.registration.JistRegistrationComposeTransMatrices$ExecuteWrapper
• de.mpg.cbs.jist.registration.JistRegistrationEmbeddedSyN
• de.mpg.cbs.jist.registration.JistRegistrationGenerateLinearMapping
• de.mpg.cbs.jist.registration.JistRegistrationGeometryBasedSurface
• de.mpg.cbs.jist.registration.JistRegistrationApplyDeformations
• de.mpg.cbs.jist.registration.JistRegistrationScannerTransform
• de.mpg.cbs.jist.registration.JistRegistrationComposeTransMatrices

The following plugins fail to generate XML:

• de.mpg.cbs.jist.segmentation.JistSegmentationProbabilityExtraction - no class definition error. Exception in thread "main" java.lang.NoClassDefFoundError: de/mpg/cbs/jist/segmentation/JistSegmentationProbabilityExtraction (wrong name: de/mpg/cbs/jist/modules/JistSegmentationProbabilityExtraction)
• de.mpg.cbs.jist.surface.JistSurfaceMgdmRepresentation - no class definition error. Exception in thread "main" java.lang.NoClassDefFoundError: de/mpg/cbs/jist/surface/JistSurfaceMgdmRepresentation (wrong name: de/mpg/cbs/jist/modules/JistSurfaceMgdmRepresentation)
• de.mpg.cbs.jist.cortex.JistCortexFullCRUISE -invalid character in cli arg. cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] -help
  cli Usage: edu.jhu.ece.iacl.jist.cli.run [classname] [run options]
  cli PARSE Error: opt contains illegal character value '/'
  java.lang.IllegalArgumentException: opt contains illegal character value '/'
  at org.apache.commons.cli.OptionValidator.validateOption(OptionValidator.java:73)
  at org.apache.commons.cli.Option.(Option.java:123)
  at org.apache.commons.cli.Options.addOption(Options.java:131)
  at org.apache.commons.cli.Options.addOption(Options.java:114)
  at edu.jhu.ece.iacl.jist.cli.JistCLI.parseParamCollection(JistCLI.java:216)
  at edu.jhu.ece.iacl.jist.cli.JistCLI.parseParamCollection(JistCLI.java:221)
  at edu.jhu.ece.iacl.jist.cli.JistCLI.(JistCLI.java:95)
  at edu.jhu.ece.iacl.jist.cli.run.main(run.java:45)

All three of these should be a quick fix.

I have something ready to go that fixes a lot of these issues. This update also tests the XML that gets generated to see whether or not it is well-formed. 

Additionally, it looks like a lot of the de modules have changed location. I am trying these now.