sct_smooth_spinalcord

Smooth the spinal cord along its centerline. Steps are:

  1. Spinal cord is straightened (using centerline),

  2. a Gaussian kernel is applied in the superior-inferior direction,

  3. then cord is de-straightened as originally.

usage: sct_smooth_spinalcord -i <file> -s <file> [-smooth <list>]
                             [-algo-fitting <str>] [-o <file>] [-h] [-v <int>]
                             [-profile-time [<file>]] [-trace-memory [<folder>]]
                             [-r {0,1}]

MANDATORY ARGUMENTS

-i

Image to smooth. Example: data.nii.gz

-s

Spinal cord centerline or segmentation. Example: data_centerline.nii.gz

OPTIONAL ARGUMENTS

-smooth

Sigma (standard deviation) of the smoothing Gaussian kernel (in mm). For isotropic smoothing you only need to specify a value (e.g. 2). For anisotropic smoothing specify a value for each axis, separated with a comma. The order should follow axes Right-Left, Antero-Posterior, Superior-Inferior (e.g.: 1,1,3). For no smoothing, set value to 0.

Default: [0, 0, 3]

-algo-fitting

Possible choices: bspline, polyfit

Algorithm for curve fitting. For more information, see sct_straighten_spinalcord.

Default: “bspline”

-o

Output filename. Example: smooth_sc.nii.gz. If not provided, the suffix _smooth will be added to the input file name.

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