<?xml version="1.0" standalone='no'?>
<!DOCTYPE MRML SYSTEM "mrml20.dtd">
<MRML>
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<Volume id='V2' name='subject001_rFLAIR' filePattern='%s' filePrefix='subject001_rFLAIR.nii.gz' fileType='Generic' rasToIjkMatrix='1 -0 0 87.5 -0 1 -0 127.5 0 -0 1 87.5 -0 0 -0 1' rasToVtkMatrix='1 -0 -0 87.5 0 -1 0 127.5 -0 0 1 87.5 -0 -0 0 1' positionMatrix='1 0 0 -87.5 0 -1 0 127.5 0 0 1 -87.5 0 0 0 1' scanOrder='IS' description='IS' colorLUT='0' fullPrefix='/Users/icsapo/Desktop/EMSegmentTutorial/subject001/subject001_rFLAIR.nii.gz' littleEndian='true' window='180' level='103' lowerThreshold='0' upperThreshold='452' imageRange='1 176' dimensions='176 256' spacing='1 1 1'></Volume>
<Volume id='V3' name='subject001_ECC' filePattern='%s' filePrefix='subject001_ECC.nii.gz' fileType='Generic' rasToIjkMatrix='1 -0 0 87.5 -0 1 -0 127.5 0 -0 1 87.5 -0 0 -0 1' rasToVtkMatrix='1 -0 -0 87.5 0 -1 0 127.5 -0 0 1 87.5 -0 -0 0 1' positionMatrix='1 0 0 -87.5 0 -1 0 127.5 0 0 1 -87.5 0 0 0 1' scanOrder='IS' description='IS' colorLUT='-1' fullPrefix='/Users/icsapo/Desktop/EMSegmentTutorial/subject001/subject001_ECC.nii.gz' labelMap='true' interpolate='false' littleEndian='true' window='2' level='0' lowerThreshold='0' upperThreshold='0' imageRange='1 176' dimensions='176 256' spacing='1 1 1'></Volume>
<Volume id='V4' name='subject001_icbmCSF' filePattern='%s' filePrefix='subject001_icbmCSF.nii.gz' fileType='Generic' rasToIjkMatrix='1 -0 0 87.5 -0 1 -0 127.5 0 -0 1 87.5 -0 0 -0 1' rasToVtkMatrix='1 -0 -0 87.5 0 -1 0 127.5 -0 0 1 87.5 -0 -0 0 1' positionMatrix='1 0 0 -87.5 0 -1 0 127.5 0 0 1 -87.5 0 0 0 1' scanOrder='IS' description='IS' colorLUT='0' fullPrefix='/Users/icsapo/Desktop/EMSegmentTutorial/subject001/subject001_icbmCSF.nii.gz' littleEndian='true' window='94' level='52' lowerThreshold='0' upperThreshold='99' imageRange='1 176' dimensions='176 256' spacing='1 1 1'></Volume>
<Volume id='V5' name='subject001_icbmGRAY' filePattern='%s' filePrefix='subject001_icbmGRAY.nii.gz' fileType='Generic' rasToIjkMatrix='1 -0 0 87.5 -0 1 -0 127.5 0 -0 1 87.5 -0 0 -0 1' rasToVtkMatrix='1 -0 -0 87.5 0 -1 0 127.5 -0 0 1 87.5 -0 -0 0 1' positionMatrix='1 0 0 -87.5 0 -1 0 127.5 0 0 1 -87.5 0 0 0 1' scanOrder='IS' description='IS' colorLUT='0' fullPrefix='/Users/icsapo/Desktop/EMSegmentTutorial/subject001/subject001_icbmGRAY.nii.gz' littleEndian='true' window='86' level='56' lowerThreshold='0' upperThreshold='99' imageRange='1 176' dimensions='176 256' spacing='1 1 1'></Volume>
<Volume id='V6' name='subject001_icbmWHITE' filePattern='%s' filePrefix='subject001_icbmWHITE.nii.gz' fileType='Generic' rasToIjkMatrix='1 -0 0 87.5 -0 1 -0 127.5 0 -0 1 87.5 -0 0 -0 1' rasToVtkMatrix='1 -0 -0 87.5 0 -1 0 127.5 -0 0 1 87.5 -0 -0 0 1' positionMatrix='1 0 0 -87.5 0 -1 0 127.5 0 0 1 -87.5 0 0 0 1' scanOrder='IS' description='IS' colorLUT='0' fullPrefix='/Users/icsapo/Desktop/EMSegmentTutorial/subject001/subject001_icbmWHITE.nii.gz' littleEndian='true' window='100' level='50' lowerThreshold='0' upperThreshold='100' imageRange='1 176' dimensions='176 256' spacing='1 1 1'></Volume>
<Segmenter MaxInputChannelDef ='2' Alpha ='0.3' SmWidth ='19' SmSigma ='9' SegmentationBoundaryMin ='1 1 1 ' SegmentationBoundaryMax ='176 256 176 ' NumberOfTrainingSamples ='100' DisplayProb  ='1'>
  <SegmenterGraph name ='2' Xmin ='10' Xmax ='260' Xsca ='50'></SegmenterGraph>
  <SegmenterGraph name ='1' Xmin ='10' Xmax ='600' Xsca ='50'></SegmenterGraph>
  <SegmenterInput name ='Channel0' FileName='subject001_MPRAGE'></SegmenterInput>
  <SegmenterInput name ='Channel1' FileName='subject001_rFLAIR'></SegmenterInput>
  <SegmenterSuperClass name='Head' Prob='1' InputChannelWeights='1.0 1.0' LocalPriorWeight='1' RegistrationCovariance='1 1 1 1 1 1 0.1 0.1 0.1 ' NumClasses ='2' PrintBias='0' PrintLabelMap='0' PrintFrequency='0' StopEMType='0' StopEMValue='0' StopEMMaxIter='4' StopMFAType='0' StopMFAValue='0' StopMFAMaxIter='2' PrintEMLabelMapConvergence='0' PrintEMWeightsConvergence='0' PrintMFALabelMapConvergence='0' PrintMFAWeightsConvergence='0' RegistrationType='0'  StopStopBiasCalculation='-1' GenerateBackgroundProbability='0' PrintShapeSimularityMeasure='0' PCAShapeModelType='0' RegistrationIndependentSubClassFlag='0'>
    <SegmenterClass name='0' Prob='0.15' InputChannelWeights='0.01 0.01' LocalPriorWeight='1' LocalPriorName='subject001_ECC' RegistrationCovariance='1 1 1 1 1 1 0.1 0.1 0.1 ' Label='0' LogMean='3.8296 2.3139' LogCovariance='0.4753 0.1581 | 0.1581 0.1682' PrintQuality='0' PCALogisticSlope ='1' PCALogisticMin ='0' PCALogisticMax ='20' PCALogisticBoundary ='9.5' PrintPCA='0'>
    </SegmenterClass>
    <SegmenterSuperClass name='ICC' Prob='0.85' InputChannelWeights='1.0 1.0' LocalPriorWeight='1' RegistrationCovariance='1 1 1 1 1 1 0.1 0.1 0.1 ' NumClasses ='3' PrintBias='0' PrintLabelMap='0' PrintFrequency='0' StopEMType='0' StopEMValue='0' StopEMMaxIter='4' StopMFAType='0' StopMFAValue='0' StopMFAMaxIter='2' PrintEMLabelMapConvergence='0' PrintEMWeightsConvergence='0' PrintMFALabelMapConvergence='0' PrintMFAWeightsConvergence='0' RegistrationType='0'  StopStopBiasCalculation='-1' GenerateBackgroundProbability='0' PrintShapeSimularityMeasure='0' PCAShapeModelType='0' RegistrationIndependentSubClassFlag='0'>
      <SegmenterClass name='4' Prob='0.6' InputChannelWeights='0.7 0.3' LocalPriorWeight='0.8' LocalPriorName='subject001_icbmGRAY' RegistrationCovariance='1 1 1 1 1 1 0.1 0.1 0.1 ' Label='4' LogMean='5.7081 4.4913' LogCovariance='0.0138 0.0078 | 0.0078 0.0867' PrintQuality='0' PCALogisticSlope ='1' PCALogisticMin ='0' PCALogisticMax ='20' PCALogisticBoundary ='9.5' PrintPCA='0'>
      </SegmenterClass>
      <SegmenterClass name='8' Prob='0.3' InputChannelWeights='0.95 0.05' LocalPriorWeight='0.08' LocalPriorName='subject001_icbmWHITE' RegistrationCovariance='1 1 1 1 1 1 0.1 0.1 0.1 ' Label='8' LogMean='6.0911 4.7596' LogCovariance='0.0123 -0.0084 | -0.0084 0.0288' PrintQuality='0' PCALogisticSlope ='1' PCALogisticMin ='0' PCALogisticMax ='20' PCALogisticBoundary ='9.5' PrintPCA='0'>
      </SegmenterClass>
      <SegmenterClass name='5' Prob='0.1' InputChannelWeights='1.0 1.0' LocalPriorWeight='0.2' LocalPriorName='subject001_icbmCSF' RegistrationCovariance='1 1 1 1 1 1 0.1 0.1 0.1 ' Label='5' LogMean='4.701 2.5164' LogCovariance='0.0538 0.0156 | 0.0156 0.0881' PrintQuality='0' PCALogisticSlope ='1' PCALogisticMin ='0' PCALogisticMax ='20' PCALogisticBoundary ='9.5' PrintPCA='0'>
      </SegmenterClass>
    </SegmenterSuperClass>
  </SegmenterSuperClass>
</Segmenter>
<Color name='Gray' labels='4' diffuseColor='0.6 0.6 0.6'></Color>
<Color name='White' labels='8' diffuseColor='0.9 0.9 0.6'></Color>
<Color name='Csf' labels='5' diffuseColor='0.4 0.6 0.9'></Color>
<Color name='Black' labels='0' diffuseColor='0 0 0'></Color>
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