sct_create_mask

Create mask along z direction.

usage: sct_create_mask -i <file> -p <str> [-size <str>]
                       [-f {cylinder,box,gaussian}] [-o <str>] [-h] [-v <int>]
                       [-profile-time [<file>]] [-trace-memory [<folder>]]
                       [-r {0,1}]

MANDATORY ARGUMENTS

-i

Image to create mask on. Only used to get header. Must be 3D. Example: data.nii.gz

-p

Process to generate mask.

  • coord,XxY: Center mask at the X,Y coordinates. Example: coord,20x15

  • point,FILE: Center mask at the X,Y coordinates of the label defined in input volume FILE. Example: point,label.nii.gz

  • center: Center mask in the middle of the FOV [nx/2, ny/2].

  • centerline,FILE: At each slice, the mask is centered at the spinal cord centerline, defined by the input segmentation FILE. Example: centerline,t2_seg.nii.gz

Default: “center”

OPTIONAL ARGUMENTS

-size

Diameter of the mask in the axial plane, given in pixel (Example: 35) or in millimeter (Example: 35mm). If shape=gaussian, size instead corresponds to “sigma” (Example: 45).

Default: “41”

-f

Possible choices: cylinder, box, gaussian

Shape of the mask

Default: “cylinder”

-o

Name of output mask, Example: data.nii.gz

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