sct_dice_coefficient

Compute the Dice Coefficient. N.B.: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.

usage: sct_dice_coefficient -i <file> -d <file> [-2d-slices {0,1,2}] [-b <list>]
                            [-bmax {0,1}] [-bzmax {0,1}] [-bin {0,1}] [-o <str>]
                            [-h] [-v <int>] [-r {0,1}]

MANDATORY ARGUMENTS

-i

First input image. Example: t2_seg.nii.gz

-d

Second input image. Example: t2_manual_seg.nii.gz

OPTIONAL ARGUMENTS

-2d-slices

Possible choices: 0, 1, 2

Compute DC on 2D slices in the specified dimension

-b

Bounding box with the coordinates of the origin and the size of the box as follow: x_origin,x_size,y_origin,y_size,z_origin,z_size. Example: 5,10,5,10,10,15

-bmax

Possible choices: 0, 1

Use maximum bounding box of the images union to compute DC.

-bzmax

Possible choices: 0, 1

Use maximum bounding box of the images union in the “Z” direction to compute DC.

-bin

Possible choices: 0, 1

Binarize image before computing DC. (Put non-zero-voxels to 1)

-o

Output file with DC results (.txt). Example: dice_coeff.txt

MISC ARGUMENTS

-v

Possible choices: 0, 1, 2

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

Default: 1

-r

Possible choices: 0, 1

Remove temporary files.

Default: 1