sct_create_mask

Create mask along z direction.

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

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. (e.g. coord,20x15)

  • point,FILE: Center mask at the X,Y coordinates of the label defined in input volume FILE. (e.g. 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. (e.g. 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

-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