Utilities (CLI only)

• BraTS Similarity Metrics Computation

This is a command line executable containing the following functionalities (with corresponding examples):

• Resizing

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -o C:/test_75.nii.gz -r 75 -ri linear

• Resampling

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/input.nii.gz -o C:/output.nii.gz -rr 1.0 -ri LINEAR
  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/input.nii.gz -o C:/output.nii.gz -rf C:/reference.nii.gz -ri LINEAR
  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/input.nii.gz -o C:/output.nii.gz -rr 1.0,2.0,3.0 -ri LINEAR
  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/inputMask.nii.gz -o C:/outputMask.nii.gz -rr 1.0,2.0,3.0 -ri LINEAR -rm 1

• Image information

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -inf
  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -inf

• Unique values in image

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -un

• Change values in image: The following command will change all voxels of value 1 & 2 to 2 & 4, respectively:

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -cv 1x2,2x4

• Get smallest bounding box in mask (optional isotropic bounding box)

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -b C:/testMask.nii.gz -o C:/output.nii.gz

• Test 2 images

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -tb C:/test.nii.gz

• Create mask from threshold

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -o C:/test.nii.gz -cm 50,1000

• DICOM to NIfTI conversion

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.dcm -o C:/test.nii.gz -d2n

• NIfTI to DICOM conversion: Note that both the NIfTI and DICOM reference images need to be defined in the same space for this to work correctly

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/imageToConvert.nii.gz -o C:/outputDicom/ -n2d C:/referenceDICOM/

• NIfTI to DICOM-Seg conversion (using DCMQI)

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/maskToConvert.nii.gz -o C:/outputDicom/ -ds C:/referenceDICOM/ -dsJ C:/dicomSeg.json

  Please see DCMQI's FAQ and use case for JSON-related information.
• Re-orient image

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output.nii.gz -or RAI

• Cast image to another pixel type

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -o C:/test_int.nii.gz -c int

• Thresholding:
  • Below

    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output.nii.gz -thB 100

  • Above

    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output.nii.gz -thA 50

  • Above & Below

    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output.nii.gz -tAB 50,100

  • Otsu

    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output.nii.gz -thO 1

  • Binary

    ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output.nii.gz -tAB 50,100 -tBn

• Convert file formats

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -o C:/test.mha -cov

• Extract Image Series from Joined stack and vice-versa (4D <-> 3D)

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output -j2e 1 # output images are written in the form C:/output_${slice}.nii.gz
  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/1.nii.gz -o C:/output/ -j2e 1 # output images are written in the form C:/output/extractedImage_${slice}.nii.gz
  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/ -o C:/output.nii.gz -e2j 1.5

• Transform coordinates from world to image and vice-versa

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -i2w 10,10,30
  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test.nii.gz -w2i 10.5,10.1,30.6

• Label similarity Metrics between 2 label images: pure mathematical formulations are given as output

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/outputMask.nii.gz -l2s C:/referenceMask.nii.gz

• BraTS similarity Metrics between 2 label images: special considerations for metrics are done in this mode because output needs to be BraTS-compliant.

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/referenceMask.nii.gz -lsb C:/test/predictedMask.nii.gz

• Collect information from all images in a directory and put it in CSV

  ${CaPTk_InstallDir}/bin/Utilities.exe -i C:/test/inputDirectory -o C:/test/inputDirectoryProperties.csv \
  -co 1 \ # enable recursion
  -cF volume \ # only process files that contain this string pattern 
  -cFE .nii.gz \ # only process files with this extension 
  -cP 0,1 \ # which properties to read; see usage for all options

For a full list of available applications and examples, please use the command:

${CaPTk_InstallDir}/bin/Utilities -h