Cancer Imaging Phenomics Toolkit (CaPTk)
1.6.2.Alpha
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This application provides a fully automatic segmentation of lung nodules and prediction of survival and nodal failure risks as a three step workflow[1].
REQUIREMENTS:
USAGE:
Step 1: Lung Field Segmentation
SBRT_LungField.exe -p C:/PET.nii.gz -c C:/CT.nii.gz -o C:/outputBasename -m C:/foregroundMask.nii.gz # optional mask
It will generate the lung field mask image with name C:/outputBasename_lf.nii.gz. The mask image will contain 2 labels, label 3 for foreground and label 2 for lung field.
Step 2: Lung Nodule Segmentation
SBRT_Nodule.exe -p C:/PET.nii.gz -c C:/CT.nii.gz -m C:/mask.nii.gz -o C:/outputBasename
It will generate two output images (seed image for nodule segmentation and nodule mask image) with names C:/outputBasename_seeds.nii.gz and C:/outputBasename_segmentation.nii.gz
SBRT_Nodule.exe -p C:/PET.nii.gz -c C:/CT.nii.gz -m C:/mask.nii.gz -o C:/outputBasename -s C:/seedImage.nii.gz
It will generate the nodule mask image with name C:/outputBasename_segmentation.nii.gz.
SBRT_Nodule.exe -p C:/PET.nii.gz -c C:/CT.nii.gz -m C:/mask.nii.gz -o C:/outputBasename -s C:/seedImage.nii.gz -l 2
"Label_value" indicates the label of lung field in the input mask image, default value is 2.
Step 3: Prognostic Modeling
This application is also available as with a stand-alone CLI for data analysts to build pipelines around, using the following example commands:
SBRT_Analysis.exe -i C:/PET.nii.gz -m C:/mask.nii.gz -l 1
It will calculate and print the predicted risks regarding survival and nodal failure.
SBRT_Analysis.exe -i C:/PET.nii.gz -m C:/mask.nii.gz -l 1 -o C:/outputFile
It will calculate and print the predicted risks regarding survival and nodal failure, it will also save the radiomic features used for the prediction into the assigned file.
Reference: