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>] [-profile-time [<file>]]
                            [-trace-memory [<folder>]] [-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

-profile-time

Enables time-based profiling of the program, dumping the results to the specified file.

If no file is specified, human-readable results are placed into a ‘time_profiling_results.txt’ document in the current directory (’/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/stable/documentation/source’). If the specified file is a .prof file, the file will instead be in binary format, ready for use with common post-profiler utilities (such as snakeviz).

-trace-memory

Enables memory tracing of the program.

When active, a measure of the peak memory (in KiB) will be output to the file peak_memory.txt. Optionally, developers can also modify the SCT code to add additional snapshot_memory() calls. These calls will ‘snapshot’ the memory usage at that moment, saving the memory trace at that point into a second file (memory_snapshots.txt).

By default, both outputs will be placed in the current directory (’/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/stable/documentation/source’). Optionally, you may provide an alternative directory (-trace-memory <dir_name>), in which case all files will be placed in that directory instead. Note that this WILL incur an overhead to runtime, so it is generally advised that you do not run this in conjunction with the time profiler or in time-sensitive contexts.

-r

Possible choices: 0, 1

Remove temporary files.

Default: 1