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