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>]
                       [-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

-r

Possible choices: 0, 1

Remove temporary files.

Default: 1