How To Guides

This section provides step-by-step guidance to apply the CaPTk functionalities:

• Pre-processing
  • DICOM to NIfTI conversion
  • Image Registration
  • Image Denoizing (SUSAN - ITK filter)
  • N3 Bias Correction (ITK filter)
  • N4 Bias Correction (ITK filter)
  • Histogram Matching
  • Z-Score Normalization
  • BraTS Pre-processing Pipeline
• Segmentation
  • Interactive Machine Learning based - Utilizing Geodesic Distance Transform and SVM
  • ITK-SNAP
  • Deep Learning based - pre-trained models offered for a) skull-stripping and b) brain tumors
• Feature Extraction
• ML Training Module
• Specialized Applications
  • Brain Cancer: Novel MRI Normalization - WhiteStripe
  • Brain Cancer: Population Atlas
  • Brain Cancer: Confetti - Diffusion track visualization
  • Brain Cancer: Glioblastoma Infiltration Index (Recurrence Predictor)
  • Brain Cancer: Glioblastoma Pseudo-progression Index
  • Brain Cancer: Glioblastoma Survival Prediction Index
  • Brain Cancer: Glioblastoma EGFRvIII Surrogate Index (PHI Estimator)
  • Brain Cancer: Glioblastoma EGFRvIII SVM Prediction
  • Breast Cancer: Breast Segmentation
  • Breast Cancer: Breast Density Estimation (LIBRA)
  • Breast Cancer: Texture Feature Extraction
  • Lung Cancer: Radiomic Analysis of Lung Cancer (SBRT Lung)
  • Miscellaneous: Directionality Estimator
  • Miscellaneous: Diffusion Derivatives
  • Miscellaneous: Perfusion Derivatives
  • Miscellaneous: Perfusion PCA Parameter Extractor
• Utilities (CLI only): Collection of helper utilities such as resampling, thresholding, image information, casting, label statistics, and more.
  • BraTS Metrics Computation

Notes:

• Training videos can be accessed in our YouTube Channel, specifically in the original and ITCR 2020 CaPTk Playlists.
• All applications are available as command-line applications (use parameter "-h" for detailed help messages).

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