sct_analyze_texture

Extraction of gray level co-occurence matrix (GLCM) texture features from an image within a given mask. The textures features are those defined in the sckit-image implementation: https://scikit-image.org/docs/dev/api/skimage.feature.html#graycoprops. This function outputs one nifti file per texture metric (contrast,dissimilarity,homogeneity,energy,correlation,ASM) and per orientation called fnameInput_feature_distance_angle.nii.gz. Also, a file averaging each metric across the angles, called fnameInput_feature_distance_mean.nii.gz, is output.

usage: sct_analyze_texture -i <file> -m <file> [-h] [-feature <str>]
                           [-distance <int>] [-angle <list>] [-dim {ax,sag,cor}]
                           [-ofolder <folder>] [-r {0,1}] [-v <int>]

MANDATORY ARGUMENTS

-i

Image to analyze. Example: t2.nii.gz

-m

Image mask Example: t2_seg.nii.gz

OPTIONALS ARGUMENTS

-feature

List of GLCM texture features (separate arguments with ,).

Default: “contrast,dissimilarity,homogeneity,energy,correlation,ASM”

-distance

Distance offset for GLCM computation, in pixel (suggested distance values between 1 and 5). Example: 1

Default: 1

-angle

List of angles for GLCM computation, separate arguments with ,, in degrees (suggested distance values between 0 and 179). Example: 0,90

Default: “0,45,90,135”

-dim

Possible choices: ax, sag, cor

Compute the texture on the axial (ax), sagittal (sag) or coronal (cor) slices.

Default: “ax”

-ofolder

Output folder. Example: /my_texture/

Default: “./texture”

-r

Possible choices: 0, 1

Remove temporary files.

Default: 1

-v

Possible choices: 0, 1, 2

Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode

Default: 1