SMILI Assistant

milxImageApp

The image application can run common image processing algorithms over a number of 3D volumes (vector images partially supported) at once. This includes:

Thresholding - Binary, Otsu, Multiple Otsu, Banded, Above and Below
Checkerboarding
Flipping Axes
Smoothing - Median, Gradient Anisotropic
Mask and Crop using Mask
Padding
Information (Direction, Origin etc.)
Label info
Resampling
Arithmetic (add, minus, difference, mean)

Example Uses

Otsu multiple threshold:

  milxImageApp --Otsu 128 features/median/*.nii.gz --labels 4 -p features/Otsu/Otsu_128bins_

Checkerboards Atlas_MRI_Mean2_R_Preprocessed_x2.nii.gz to all Nifti images in current directory and writes to files with prefix check_:

  milxImageApp --checkerboard SyngoHipData/Atlas_MRI_Mean2_R_Preprocessed_x2.nii.gz *.nii.gz -p check_

Rescale image intensities:

  milxImageApp --rescale MRIs/*.nii.gz --above 255 --below 0 -p features/rescale/rescale_