Cancer Imaging Phenomics Toolkit (CaPTk)  1.3.0
Stand Alone CLIs

Overview | Pre-Processing | Interaction | Segmentation | Quantitative Imaging Feature Panel | Specialized Applications | Stand Alone CLIs

Some of the applications also have a stand-alone CLI for scripting/batch-processing needs. We are continuously adding more applications to this list.

Application Usage Example
Geodesic Segmentation GeodesicSegmentation.exe -i C:/inputImage.nii.gz -m C:/maskWithOneLabel.nii.gz -o C:/outputImage.nii.gz -t 20
WhiteStripe Normalization WhiteStripe.exe -i C:/inputImage.nii.gz -o C:/outputImage.nii.gz
EGFRvIII Surrogate Index EGFRvIIISurrogateIndex.exe -i C:/inputImage.nii.gz -m C:/maskWithNearAndFarLabels.nii.gz
SBRT Lung Segmentation SBRT_Lung_Segment.exe -d C:/dataDir
SBRT Lung Analyze SBRT_Lung_Analyze.exe -c C:/CTImage.nii.gz -p C:/PETImage.nii.gz -m C:/mask.nii.gz -t C:/TrainedModel.xml -o C:/output.txt
LIBRA LIBRA.exe –input C:/inputDICOMDir –output C:/outputDir
Directionality Estimation DirectionalityEstimate.exe -l C:/labelMap.nii.gz -o C:/output.txt -i 40,25,60
Feature Extraction FeatureExtraction.exe -s "AAC0_timestamp" -p "path/T1,path/T2,path/mask" -m "T1/T2" -r "2,4,5" -l "ED,EN,NE" -f "GLCM,GLRM" -fGLCM "radius=4,angle=0::45:180"
FeatureExtraction.exe -i "file.csv" -m "T1/T2" -r "2,4,5" -l "ED,EN,NE" -fi "myparam.csv"
  • Generation of connectivity signatures of the fibers that will be clustered into bundles:
    Confetti signature -i tdi_paths_freesurfer_87ROIs.csv -f fibers.Bfloat -o signatures.csv
  • Clustering of the generated fibers into bundles:
    Confetti cluster -s signatures.csv -k 200 -o clusterIDs.csv
  • Identification of specific tracts (requires an annotated example):
    Confetti extract -t template/ -f fibers.Bfloat -c clusterIDs.csv -o tracts_

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