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Texture

Scripting example (simple series) v5.10

Download these data files (here):

  • DataFile1_PT_Anonym.zip
  • DataFile1_PT_Anonym_RoiVolume_healthy.nii
  • DataFile1_PT_Anonym_RoiVolume_tumor.nii
  • DataFile1_PT_Anonym_TextureResults.cvs

 

Unzip the DataFile1_PT_Anonym.zip

Create the script file DataFile1_PT_Anonym_script.txt (see example of script below).

Edit the script and remplace all the "WD" by your working directory:

  • ex on Linux: WD=/home/me/LIFExControlQualitySet
  • ex on Mac: WD=/home/me/LIFExControlQualitySet
  • ex on Windows: WD=C:/Users/me/LIFExControlQualitySet

 

Run: 

  1. drag and drop the script file into LIFEx (left side after having selected texture protocol)
  2. results are saved in DataFile1_PT_Anonym_TextureResults.csv
  3. check results with our DataFile1_PT_Anonym_TextureResults.csv file 

 

Here, an example of script (save in txt format, not rtf):

#Common
LIFEx.texture.BinSize=3.125
LIFEx.texture.NbGrey=64.0
LIFEx.texture.SessionCsv=WD/DataFiles/DataFile1_PTCT/DataFile1_PT_Anonym_TextureResults_LIFEx5.60.csv

# Absolute
LIFEx.texture.ButtonAbsolute=true
LIFEx.texture.MinBound=0.0
LIFEx.texture.MaxBound=20.0

# RelativeMeanSd
LIFEx.texture.ButtonRelativeMeanSd=false

# RelativeMinMax
LIFEx.texture.ButtonRelativeMinMax=false

# GLCM
LIFEx.texture.GLCM.DistanceWithNeighbours=1

# SpatialResampling (0 = no spatial resampling = native spacing voxels)
LIFEx.texture.ZSpatialResampling=0
LIFEx.texture.YSpatialResampling=0
LIFEx.texture.XSpatialResampling=0

# Patient0
LIFEx.texture.Img0=WD/DataFiles/DataFile1_PTCT/DataFile1_PT_Anonym
LIFEx.texture.Img0Roi0=WD/DataFiles/DataFile1_PTCT/DataFile1_PT_Anonym_RoiVolume_healthy.nii
LIFEx.texture.Img0Roi1=WD/DataFiles/DataFile1_PTCT/DataFile1_PT_Anonym_RoiVolume_tumor.nii

Scripting example (simple series) v6.09

Download these data files (here):

  • DataFile1_PT_Anonym.zip
  • DataFile1_PT_Anonym_RoiVolume_healthy.nii
  • DataFile1_PT_Anonym_RoiVolume_tumor.nii

 

Unzip the DataFile1_PT_Anonym.zip

Create the script file Texture_script.txt (see example of script below).

Edit the script and remplace all the "WD" by your working directory:

  • ex on Linux: WD=/home/me/LIFExControlQualitySet
  • ex on Mac: WD=/home/me/LIFExControlQualitySet
  • ex on Windows: WD=C:/Users/me/LIFExControlQualitySet

 

Run: 

  1. drag and drop the script file into LIFEx (left side after having selected texture protocol)
  2. results are saved in TextureResults.csv

 

Here, an example of script (save in txt format, not rtf):

#Common
LIFEx.texture.BinSize=2
LIFEx.texture.NbGrey=10
LIFEx.texture.SessionCsv=WD/DataFiles/DataFile1_PTCT/TextureResults.csv

# Absolute
LIFEx.texture.ButtonAbsolute=true
LIFEx.texture.MinBound=0.0
LIFEx.texture.MaxBound=20.0

# RelativeMeanSd
LIFEx.texture.ButtonRelativeMeanSd=false

# RelativeMinMax
LIFEx.texture.ButtonRelativeMinMax=false

# GLCM
LIFEx.texture.GLCM.DistanceWithNeighbours=1

# SpatialResampling (0 = no spatial resampling = native spacing voxels)
LIFEx.texture.ZSpatialResampling=0
LIFEx.texture.YSpatialResampling=0
LIFEx.texture.XSpatialResampling=0

# Laplacian of Gaussian filter (LIFEx>=6.09)
#LIFEx.texture.LaplacianDimensionProcessing=3D
#LIFEx.texture.LaplacianSigma.z=0.8
#LIFEx.texture.LaplacianSigma.y=0.8
#LIFEx.texture.LaplacianSigma.x=0.8

# Patient0
LIFEx.texture.Img0=WD/DataFiles/DataFile1_PTCT/DataFile1_PT_Anonym
LIFEx.texture.Img0Roi0=WD/DataFiles/DataFile1_PTCT/DataFile1_PT_Anonym_RoiVolume_healthy.nii
LIFEx.texture.Img0Roi1=WD/DataFiles/DataFile1_PTCT/DataFile1_PT_Anonym_RoiVolume_tumor.nii

Scripting example (multiples series) v5.10

Download these data files (here):

  • DataFile1_PT_Anonym.zip
  • DataFile1_PT_Anonym_RoiVolume_healthy.nii.zip
  • DataFile1_PT_Anonym_RoiVolume_tumor.nii.zip
  • DataFile1_PT_Anonym_LIFEx5.60_Texture_SimpleSeries_Results.csv

 

Unzip all zip files.

Create the script file DataFile1_PT_Anonym_LIFEx5.60_Texture_SimpleSeries_Script.txt (see example of script below).

Edit the script and remplace all the "WD" by your working directory:

  • ex on Linux: WD=/home/me/LIFExControlQualitySet
  • ex on Mac: WD=/home/me/LIFExControlQualitySet
  • ex on Windows: WD=C:/Users/me/LIFExControlQualitySet

 

Run: 

  1. drag and drop the script file into LIFEx (left side after having selected texture protocol)
  2. results are saved in DataFile1_PT_Anonym_LIFEx5.60_Texture_SimpleSeries_YourResults.csv
  3. check results with our DataFile1_PT_Anonym_LIFEx5.60_Texture_SimpleSeries_Results.csv file 

 

Here, an example of script (save in txt format, not rtf):

#Common
LIFEx.texture.BinSize=3.125
LIFEx.texture.NbGrey=64.0
LIFEx.texture.SessionCsv=WD/DataFile1_PT_Anonym_TextureResults.csv

# Absolute
LIFEx.texture.ButtonAbsolute=true
LIFEx.texture.MinBound=0.0
LIFEx.texture.MaxBound=20.0

# RelativeMeanSd
LIFEx.texture.ButtonRelativeMeanSd=false

# RelativeMinMax
LIFEx.texture.ButtonRelativeMinMax=false

# SpatialResampling (0 = no spatial resampling = native spacing voxels)
LIFEx.texture.ZSpatialResampling=0
LIFEx.texture.YSpatialResampling=0
LIFEx.texture.XSpatialResampling=0

# GLCM
LIFEx.texture.GLCM.DistanceWithNeighbours=1

# Patient0
LIFEx.texture.Img0=WD/DataFile1_PT_Anonym
LIFEx.texture.Img0Roi0=WD/DataFile1_PT_Anonym_RoiVolume_healthy.nii
LIFEx.texture.Img0Roi1=WD/DataFile1_PT_Anonym_RoiVolume_tumor.nii
 

Scripting example (multiples series) v6.09

Download these data files (here):

  • DataFile1_PT_Anonym.zip
  • DataFile1_PT_Anonym_RoiVolume_healthy.nii.zip
  • DataFile1_PT_Anonym_RoiVolume_tumor.nii.zip

 

Unzip all zip files.

Create the script file Texture_Script.txt (see example of script below).

Edit the script and remplace all the "WD" by your working directory:

  • ex on Linux: WD=/home/me/LIFExControlQualitySet
  • ex on Mac: WD=/home/me/LIFExControlQualitySet
  • ex on Windows: WD=C:/Users/me/LIFExControlQualitySet

 

Run: 

  1. drag and drop the script file into LIFEx (left side after having selected texture protocol)
  2. results are saved in DataFile1_PT_Anonym_TextureResults.csv

 

Here, an example of script (save in txt format, not rtf):

#Common
LIFEx.texture.BinSize=2
LIFEx.texture.NbGrey=10
LIFEx.texture.SessionCsv=WD/DataFile1_PT_Anonym_TextureResults.csv

# Absolute
LIFEx.texture.ButtonAbsolute=true
LIFEx.texture.MinBound=0.0
LIFEx.texture.MaxBound=20.0

# RelativeMeanSd
LIFEx.texture.ButtonRelativeMeanSd=false

# RelativeMinMax
LIFEx.texture.ButtonRelativeMinMax=false

# SpatialResampling (0 = no spatial resampling = native spacing voxels)
LIFEx.texture.ZSpatialResampling=0
LIFEx.texture.YSpatialResampling=0
LIFEx.texture.XSpatialResampling=0

# Laplacian of Gaussian filter (LIFEx>=6.09)
#LIFEx.texture.LaplacianDimensionProcessing=3D
#LIFEx.texture.LaplacianSigma.z=0.8
#LIFEx.texture.LaplacianSigma.y=0.8
#LIFEx.texture.LaplacianSigma.x=0.8

# GLCM
LIFEx.texture.GLCM.DistanceWithNeighbours=1

# Patient0
LIFEx.texture.Img0=WD/DataFile1_PT_Anonym
LIFEx.texture.Img0Roi0=WD/DataFile1_PT_Anonym_RoiVolume_healthy.nii
LIFEx.texture.Img0Roi1=WD/DataFile1_PT_Anonym_RoiVolume_tumor.nii

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